I've tested with Debian Sarge 3.1r0 and agpgart was able to detected and set agp aperture correctly, with kernel 2.6.8-11-amd64-k8 Follows dmesg output from Debian:

Bootdata ok (command line is root=/dev/hdb1 ro )
Linux version 2.6.8-11-amd64-k8 (root@firetheft) (gcc version 3.4.4 20050314 (prerelease) (Debian 3.4.3-13)) #1 Mon May 30 22:15:15 UTC 2005
BIOS-provided physical RAM map:
 BIOS-e820: 0000000000000000 - 000000000009fc00 (usable)
 BIOS-e820: 000000000009fc00 - 00000000000a0000 (reserved)
 BIOS-e820: 00000000000e4000 - 0000000000100000 (reserved)
 BIOS-e820: 0000000000100000 - 000000003ffb0000 (usable)
 BIOS-e820: 000000003ffb0000 - 000000003ffc0000 (ACPI data)
 BIOS-e820: 000000003ffc0000 - 000000003fff0000 (ACPI NVS)
 BIOS-e820: 000000003fff0000 - 0000000040000000 (reserved)
 BIOS-e820: 00000000ff780000 - 0000000100000000 (reserved)
No mptable found.
On node 0 totalpages: 262064
  DMA zone: 4096 pages, LIFO batch:1
  Normal zone: 257968 pages, LIFO batch:16
  HighMem zone: 0 pages, LIFO batch:1
ACPI: RSDP (v000 ACPIAM                                    ) @ 0x00000000000fab00
ACPI: RSDT (v001 A M I  OEMRSDT  0x02000616 MSFT 0x00000097) @ 0x000000003ffb0000
ACPI: FADT (v001 A M I  OEMFACP  0x02000616 MSFT 0x00000097) @ 0x000000003ffb0200
ACPI: MADT (v001 A M I  OEMAPIC  0x02000616 MSFT 0x00000097) @ 0x000000003ffb0390
ACPI: OEMB (v001 A M I  OEMBIOS  0x02000616 MSFT 0x00000097) @ 0x000000003ffc0040
ACPI: DSDT (v001  A0232 A0232008 0x00000008 MSFT 0x0100000d) @ 0x0000000000000000
ACPI: Local APIC address 0xfee00000
ACPI: LAPIC (acpi_id[0x01] lapic_id[0x00] enabled)
Processor #0 15:12 APIC version 16
ACPI: IOAPIC (id[0x01] address[0xfec00000] gsi_base[0])
IOAPIC[0]: Assigned apic_id 1
IOAPIC[0]: apic_id 1, version 3, address 0xfec00000, GSI 0-23
ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 dfl dfl)
ACPI: IRQ0 used by override.
ACPI: IRQ2 used by override.
ACPI: IRQ9 used by override.
Using ACPI (MADT) for SMP configuration information
Checking aperture...
CPU 0: aperture @ e0000000 size 32 MB
Aperture from northbridge cpu 0 too small (32 MB)
AGP bridge at 00:00:00
Aperture from AGP @ e0000000 size 128 MB (APSIZE f20)
Built 1 zonelists
Kernel command line: root=/dev/hdb1 ro  console=tty0
Initializing CPU#0
PID hash table entries: 16 (order 4: 256 bytes)
time.c: Using 1.193182 MHz PIT timer.
time.c: Detected 2000.101 MHz processor.
Console: colour VGA+ 80x25
Dentry cache hash table entries: 262144 (order: 9, 2097152 bytes)
Inode-cache hash table entries: 131072 (order: 8, 1048576 bytes)
Memory: 1023024k/1048256k available (1586k kernel code, 24460k reserved, 901k data, 124k init)
Calibrating delay loop... 3923.96 BogoMIPS
Security Scaffold v1.0.0 initialized
Capability LSM initialized
Mount-cache hash table entries: 256 (order: 0, 4096 bytes)
CPU: L1 I Cache: 64K (64 bytes/line), D cache 64K (64 bytes/line)
CPU: L2 Cache: 512K (64 bytes/line)
CPU: AMD Athlon(tm) 64 Processor 3000+ stepping 02
Using local APIC NMI watchdog using perfctr0
ENABLING IO-APIC IRQs
init IO_APIC IRQs
 IO-APIC (apicid-pin) 1-0, 1-16, 1-17, 1-18, 1-19, 1-20, 1-21, 1-22, 1-23 not connected.
..TIMER: vector=0x31 pin1=2 pin2=-1
Using local APIC timer interrupts.
Detected 12.500 MHz APIC timer.
checking if image is initramfs...it isn't (ungzip failed); looks like an initrd
NET: Registered protocol family 16
PCI: Using configuration type 1
mtrr: v2.0 (20020519)
ACPI: Subsystem revision 20040326
ACPI: Interpreter enabled
ACPI: Using IOAPIC for interrupt routing
ACPI: PCI Root Bridge [PCI0] (00:00)
PCI: Probing PCI hardware (bus 00)
ACPI: PCI Interrupt Routing Table [\_SB_.PCI0._PRT]
ACPI: PCI Interrupt Link [LNKA] (IRQs 3 4 5 7 10 *11 14 15)
ACPI: PCI Interrupt Link [LNKB] (IRQs 3 4 5 7 *10 11 14 15)
ACPI: PCI Interrupt Link [LNKC] (IRQs 3 4 *5 7 10 11 14 15)
ACPI: PCI Interrupt Link [LNKD] (IRQs 3 4 5 7 10 11 14 15) *0, disabled.
ACPI: PCI Interrupt Link [LNKE] (IRQs 3 4 5 7 10 11 14 15) *0, disabled.
ACPI: PCI Interrupt Link [LNKF] (IRQs 3 4 5 7 10 11 14 15) *0, disabled.
ACPI: PCI Interrupt Link [LNKG] (IRQs 3 4 5 7 10 11 14 15) *0, disabled.
ACPI: PCI Interrupt Link [LNKH] (IRQs 3 4 5 7 10 11 14 15) *0, disabled.
usbcore: registered new driver usbfs
usbcore: registered new driver hub
PCI: Using ACPI for IRQ routing
IOAPIC[0]: Set PCI routing entry (1-18 -> 0xa9 -> IRQ 18 Mode:1 Active:1)
ACPI: PCI interrupt 0000:00:0d.0[A] -> GSI 18 (level, low) -> IRQ 18
IOAPIC[0]: Set PCI routing entry (1-20 -> 0xb1 -> IRQ 20 Mode:1 Active:1)
ACPI: PCI interrupt 0000:00:0f.0[B] -> GSI 20 (level, low) -> IRQ 20
ACPI: PCI interrupt 0000:00:0f.1[A] -> GSI 20 (level, low) -> IRQ 20
IOAPIC[0]: Set PCI routing entry (1-21 -> 0xb9 -> IRQ 21 Mode:1 Active:1)
ACPI: PCI interrupt 0000:00:10.0[A] -> GSI 21 (level, low) -> IRQ 21
ACPI: PCI interrupt 0000:00:10.4[C] -> GSI 21 (level, low) -> IRQ 21
IOAPIC[0]: Set PCI routing entry (1-23 -> 0xc1 -> IRQ 23 Mode:1 Active:1)
ACPI: PCI interrupt 0000:00:12.0[A] -> GSI 23 (level, low) -> IRQ 23
IOAPIC[0]: Set PCI routing entry (1-16 -> 0xc9 -> IRQ 16 Mode:1 Active:1)
ACPI: PCI interrupt 0000:01:00.0[A] -> GSI 16 (level, low) -> IRQ 16
number of MP IRQ sources: 15.
number of IO-APIC #1 registers: 24.
testing the IO APIC.......................

IO APIC #1......
.... register #00: 01000000
.......    : physical APIC id: 01
.... register #01: 00178003
.......     : max redirection entries: 0017
.......     : PRQ implemented: 1
.......     : IO APIC version: 0003
.... IRQ redirection table:
 NR Log Phy Mask Trig IRR Pol Stat Dest Deli Vect:   
 00 000 00  1    0    0   0   0    0    0    00
 01 001 01  0    0    0   0   0    1    1    39
 02 001 01  0    0    0   0   0    1    1    31
 03 001 01  0    0    0   0   0    1    1    41
 04 001 01  0    0    0   0   0    1    1    49
 05 001 01  0    0    0   0   0    1    1    51
 06 001 01  0    0    0   0   0    1    1    59
 07 001 01  0    0    0   0   0    1    1    61
 08 001 01  0    0    0   0   0    1    1    69
 09 001 01  0    1    0   1   0    1    1    71
 0a 001 01  0    0    0   0   0    1    1    79
 0b 001 01  0    0    0   0   0    1    1    81
 0c 001 01  0    0    0   0   0    1    1    89
 0d 001 01  0    0    0   0   0    1    1    91
 0e 001 01  0    0    0   0   0    1    1    99
 0f 001 01  0    0    0   0   0    1    1    A1
 10 001 01  1    1    0   1   0    1    1    C9
 11 000 00  1    0    0   0   0    0    0    00
 12 001 01  1    1    0   1   0    1    1    A9
 13 000 00  1    0    0   0   0    0    0    00
 14 001 01  1    1    0   1   0    1    1    B1
 15 001 01  1    1    0   1   0    1    1    B9
 16 000 00  1    0    0   0   0    0    0    00
 17 001 01  1    1    0   1   0    1    1    C1
IRQ to pin mappings:
IRQ0 -> 0:2
IRQ1 -> 0:1
IRQ3 -> 0:3
IRQ4 -> 0:4
IRQ5 -> 0:5
IRQ6 -> 0:6
IRQ7 -> 0:7
IRQ8 -> 0:8
IRQ9 -> 0:9
IRQ10 -> 0:10
IRQ11 -> 0:11
IRQ12 -> 0:12
IRQ13 -> 0:13
IRQ14 -> 0:14
IRQ15 -> 0:15
IRQ16 -> 0:16
IRQ18 -> 0:18
IRQ20 -> 0:20
IRQ21 -> 0:21
IRQ23 -> 0:23
.................................... done.
agpgart: Detected AGP bridge 0
agpgart: Maximum main memory to use for agp memory: 941M
agpgart: AGP aperture is 128M @ 0xe0000000
PCI-DMA: Disabling IOMMU.
IA32 emulation $Id: sys_ia32.c,v 1.32 2002/03/24 13:02:28 ak Exp $
VFS: Disk quotas dquot_6.5.1
Dquot-cache hash table entries: 512 (order 0, 4096 bytes)
devfs: 2004-01-31 Richard Gooch (<email address hidden>)
devfs: boot_options: 0x0
Initializing Cryptographic API
PCI: Via IRQ fixup for 0000:00:10.0, from 11 to 5
Linux agpgart interface v0.100 (c) Dave Jones
Serial: 8250/16550 driver $Revision: 1.90 $ 48 ports, IRQ sharing enabled
ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A
RAMDISK driver initialized: 16 RAM disks of 65536K size 1024 blocksize
serio: i8042 AUX port at 0x60,0x64 irq 12
serio: i8042 KBD port at 0x60,0x64 irq 1
input: AT Translated Set 2 keyboard on isa0060/serio0
NET: Registered protocol family 2
IP: routing cache hash table of 8192 buckets, 64Kbytes
TCP: Hash tables configured (established 262144 bind 65536)
NET: Registered protocol family 8
NET: Registered protocol family 20
ACPI: (supports S0 S1 S3 S4 S5)
RAMDISK: cramfs filesystem found at block 0
RAMDISK: Loading 4056 blocks [1 disk] into ram disk... |/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/done.
VFS: Mounted root (cramfs filesystem) readonly.
Freeing unused kernel memory: 124k freed
vesafb: probe of vesafb0 failed with error -6
NET: Registered protocol family 1
Uniform Multi-Platform E-IDE driver Revision: 7.00alpha2
ide: Assuming 33MHz system bus speed for PIO modes; override with idebus=xx
VP_IDE: IDE controller at PCI slot 0000:00:0f.1
ACPI: PCI interrupt 0000:00:0f.1[A] -> GSI 20 (level, low) -> IRQ 20
VP_IDE: chipset revision 6
VP_IDE: not 100% native mode: will probe irqs later
VP_IDE: VIA vt8237 (rev 00) IDE UDMA133 controller on pci0000:00:0f.1
    ide0: BM-DMA at 0xfc00-0xfc07, BIOS settings: hda:DMA, hdb:DMA
    ide1: BM-DMA at 0xfc08-0xfc0f, BIOS settings: hdc:DMA, hdd:pio
hda: SAMSUNG SP0411N, ATA DISK drive
hdb: SAMSUNG SP0802N, ATA DISK drive
Using anticipatory io scheduler
ide0 at 0x1f0-0x1f7,0x3f6 on irq 14
hda: max request size: 1024KiB
hda: 78242976 sectors (40060 MB) w/2048KiB Cache, CHS=16383/255/63, UDMA(100)
 /dev/ide/host0/bus0/target0/lun0: p1 p2 p3 p4
hdb: max request size: 1024KiB
hdb: 156368016 sectors (80060 MB) w/2048KiB Cache, CHS=16383/255/63, UDMA(100)
 /dev/ide/host0/bus0/target1/lun0: p1 p2 p3
hdc: SONY DVD RW DRU-710A, ATAPI CD/DVD-ROM drive
ide1 at 0x170-0x177,0x376 on irq 15
kjournald starting.  Commit interval 5 seconds
EXT3-fs: mounted filesystem with ordered data mode.
Adding 2096472k swap on /dev/hda2.  Priority:-1 extents:1
EXT3 FS on hdb1, internal journal
hdc: ATAPI 48X DVD-ROM DVD-R CD-R/RW drive, 2048kB Cache
Uniform CD-ROM driver Revision: 3.20
kjournald starting.  Commit interval 5 seconds
EXT3 FS on hdb3, internal journal
EXT3-fs: mounted filesystem with ordered data mode.
kjournald starting.  Commit interval 5 seconds
EXT3 FS on hda1, internal journal
EXT3-fs: mounted filesystem with ordered data mode.
kjournald starting.  Commit interval 5 seconds
EXT3 FS on hda3, internal journal
EXT3-fs: mounted filesystem with ordered data mode.
kjournald starting.  Commit interval 5 seconds
EXT3 FS on hda4, internal journal
EXT3-fs: mounted filesystem with ordered data mode.
via-rhine.c:v1.10-LK1.1.20-2.6 May-23-2004 Written by Donald Becker
ACPI: PCI interrupt 0000:00:12.0[A] -> GSI 23 (level, low) -> IRQ 23
eth0: VIA Rhine II at 0xa800, 00:13:d4:de:3b:1b, IRQ 23.
eth0: MII PHY found at address 1, status 0x786d advertising 01e1 Link 45e1.
SCSI subsystem initialized
libata version 1.02 loaded.
sata_via version 0.20
ACPI: PCI interrupt 0000:00:0f.0[B] -> GSI 20 (level, low) -> IRQ 20
sata_via(0000:00:0f.0): routed to hard irq line 10
ata1: SATA max UDMA/133 cmd 0xD000 ctl 0xC802 bmdma 0xB800 irq 20
ata2: SATA max UDMA/133 cmd 0xC400 ctl 0xC002 bmdma 0xB808 irq 20
ata1: no device found (phy stat 00000000)
scsi0 : sata_via
ata2: no device found (phy stat 00000000)
scsi1 : sata_via
USB Universal Host Controller Interface driver v2.2
ACPI: PCI interrupt 0000:00:10.0[A] -> GSI 21 (level, low) -> IRQ 21
uhci_hcd 0000:00:10.0: VIA Technologies, Inc. VT82xxxxx UHCI USB 1.1 Controller
uhci_hcd 0000:00:10.0: irq 21, io base 000000000000b000
uhci_hcd 0000:00:10.0: new USB bus registered, assigned bus number 1
hub 1-0:1.0: USB hub found
hub 1-0:1.0: 2 ports detected
ACPI: PCI interrupt 0000:00:10.4[C] -> GSI 21 (level, low) -> IRQ 21
ehci_hcd 0000:00:10.4: VIA Technologies, Inc. USB 2.0
ehci_hcd 0000:00:10.4: irq 21, pci mem ffffff0000161000
ehci_hcd 0000:00:10.4: new USB bus registered, assigned bus number 2
ehci_hcd 0000:00:10.4: USB 2.0 enabled, EHCI 1.00, driver 2004-May-10
hub 2-0:1.0: USB hub found
hub 2-0:1.0: 2 ports detected
usb 1-1: new low speed USB device using address 2
usb 1-2: new full speed USB device using address 3
usbcore: registered new driver hiddev
input: USB HID v1.11 Mouse [Microsoft Microsoft IntelliMouse Explorer] on usb-0000:00:10.0-1
usbcore: registered new driver usbhid
drivers/usb/input/hid-core.c: v2.0:USB HID core driver
mice: PS/2 mouse device common for all mice
ts: Compaq touchscreen protocol output
ACPI: PCI interrupt 0000:00:0d.0[A] -> GSI 18 (level, low) -> IRQ 18
ioctl32(amixer:2174): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2177): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2180): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2190): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2201): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2204): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2207): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2210): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2213): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2216): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd90c) on /dev/snd/controlC0
ioctl32(amixer:2219): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2222): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2225): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd91c) on /dev/snd/controlC0
ioctl32(amixer:2228): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd90c) on /dev/snd/controlC0
ioctl32(amixer:2231): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd90c) on /dev/snd/controlC0
ioctl32(amixer:2234): Unknown cmd fd(3) cmd(80045500){00} arg(ffffd90c) on /dev/snd/controlC0
gameport: pci0000:00:0d.1 speed 1022 kHz
eth0: Setting full-duplex based on MII #1 link partner capability of 45e1.