It happened again. What I did:

 - (it is a system with precise 12.04 LTS installed)
 - removed /.rpmdb/ (I did it just for fun, without any reason)
 - made sure /.rpmdb/ is not here
 - installed updates with update-manager
 - One day later, I checked /.rpmdb/ and it was there again.

ls '--time-style=+%Y-%m-%d %H:%M:%S' -l /.rpmdb/
insgesamt 4648
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Basenames
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Conflictname
-rw-r--r-- 1 root root    24576 2013-03-23 14:05:16 __db.001
-rw-r--r-- 1 root root  3850240 2013-03-23 14:05:16 __db.002
-rw-r--r-- 1 root root 83894272 2013-03-23 14:05:16 __db.003
-rw-r--r-- 1 root root   565248 2013-03-23 14:05:16 __db.004
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Dirnames
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Group
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Installtid
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Name
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Obsoletename
-rw-r--r-- 1 root root    12288 2013-03-23 14:04:03 Packages
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Providename
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Requirename
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Sha1header
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Sigmd5
-rw-r--r-- 1 root root     8192 2013-03-23 14:04:04 Triggername

snippet from /var/log/dpkg.log:
2013-03-23 14:03:58 configure libudev0 175-0ubuntu9.3 <none>
2013-03-23 14:03:58 status unpacked libudev0 175-0ubuntu9.3
2013-03-23 14:03:58 status half-configured libudev0 175-0ubuntu9.3
2013-03-23 14:03:58 status installed libudev0 175-0ubuntu9.3
2013-03-23 14:03:59 configure libgudev-1.0-0 1:175-0ubuntu9.3 <none>
2013-03-23 14:03:59 status unpacked libgudev-1.0-0 1:175-0ubuntu9.3
2013-03-23 14:03:59 status half-configured libgudev-1.0-0 1:175-0ubuntu9.3
2013-03-23 14:04:00 status installed libgudev-1.0-0 1:175-0ubuntu9.3
2013-03-23 14:04:00 configure linux-image-3.2.0-39-generic 3.2.0-39.62 <none>
2013-03-23 14:04:00 status unpacked linux-image-3.2.0-39-generic 3.2.0-39.62
2013-03-23 14:04:00 status half-configured linux-image-3.2.0-39-generic 3.2.0-39.62
2013-03-23 14:05:06 status installed linux-image-3.2.0-39-generic 3.2.0-39.62
2013-03-23 14:05:07 configure udev 175-0ubuntu9.3 <none>
2013-03-23 14:05:07 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:07 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:07 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:08 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:08 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:08 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:08 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:09 status unpacked udev 175-0ubuntu9.3
2013-03-23 14:05:09 status half-configured udev 175-0ubuntu9.3
2013-03-23 14:05:10 status installed udev 175-0ubuntu9.3
2013-03-23 14:05:10 status triggers-pending initramfs-tools 0.99ubuntu13.1
2013-03-23 14:05:11 configure iptables 1.4.12-1ubuntu5 <none>
2013-03-23 14:05:11 status unpacked iptables 1.4.12-1ubuntu5
2013-03-23 14:05:11 status half-configured iptables 1.4.12-1ubuntu5
2013-03-23 14:05:12 status installed iptables 1.4.12-1ubuntu5
2013-03-23 14:05:13 configure gir1.2-gudev-1.0 175-0ubuntu9.3 <none>
2013-03-23 14:05:13 status unpacked gir1.2-gudev-1.0 175-0ubuntu9.3
2013-03-23 14:05:13 status half-configured gir1.2-gudev-1.0 175-0ubuntu9.3
2013-03-23 14:05:13 status installed gir1.2-gudev-1.0 175-0ubuntu9.3
2013-03-23 14:05:14 configure linux-headers-3.2.0-39 3.2.0-39.62 <none>
2013-03-23 14:05:14 status unpacked linux-headers-3.2.0-39 3.2.0-39.62
2013-03-23 14:05:14 status half-configured linux-headers-3.2.0-39 3.2.0-39.62
2013-03-23 14:05:15 status installed linux-headers-3.2.0-39 3.2.0-39.62
2013-03-23 14:05:15 configure linux-headers-3.2.0-39-generic 3.2.0-39.62 <none>
2013-03-23 14:05:15 status unpacked linux-headers-3.2.0-39-generic 3.2.0-39.62
2013-03-23 14:05:15 status half-configured linux-headers-3.2.0-39-generic 3.2.0-39.62
2013-03-23 14:05:16 status installed linux-headers-3.2.0-39-generic 3.2.0-39.62
2013-03-23 14:05:16 configure linux-headers-generic 3.2.0.39.47 <none>
2013-03-23 14:05:16 status unpacked linux-headers-generic 3.2.0.39.47
2013-03-23 14:05:16 status half-configured linux-headers-generic 3.2.0.39.47
2013-03-23 14:05:17 status installed linux-headers-generic 3.2.0.39.47
2013-03-23 14:05:17 configure linux-image-generic 3.2.0.39.47 <none>
2013-03-23 14:05:17 status unpacked linux-image-generic 3.2.0.39.47
2013-03-23 14:05:17 status half-configured linux-image-generic 3.2.0.39.47
2013-03-23 14:05:18 status installed linux-image-generic 3.2.0.39.47
2013-03-23 14:05:18 configure linux-libc-dev 3.2.0-39.62 <none>
2013-03-23 14:05:18 status unpacked linux-libc-dev 3.2.0-39.62
2013-03-23 14:05:18 status half-configured linux-libc-dev 3.2.0-39.62
2013-03-23 14:05:18 status installed linux-libc-dev 3.2.0-39.62
2013-03-23 14:05:19 configure perl-modules 5.14.2-6ubuntu2.3 <none>
2013-03-23 14:05:19 status unpacked perl-modules 5.14.2-6ubuntu2.3
2013-03-23 14:05:19 status unpacked perl-modules 5.14.2-6ubuntu2.3
2013-03-23 14:05:19 status half-configured perl-modules 5.14.2-6ubuntu2.3

So I come to the clue that linux-image-3.2.0-39-generic(3.2.0-39.62) or linux-headers-generic(3.2.0-39.62->3.2.0.39.47) were responsible, or any package triggered by those, like dkms, initramfs etc.

Unfortunately, I did an update to raring 13.04 after the update, so the following commands didn't run on the same package versions:

find /etc/kernel:
/etc/kernel
/etc/kernel/postinst.d
/etc/kernel/postinst.d/nvidia-common.dpkg-remove
/etc/kernel/postinst.d/dkms
/etc/kernel/postinst.d/pm-utils
/etc/kernel/postinst.d/zz-update-grub
/etc/kernel/postinst.d/update-notifier
/etc/kernel/postinst.d/initramfs-tools
/etc/kernel/postinst.d/apt-auto-removal
/etc/kernel/postrm.d
/etc/kernel/postrm.d/zz-update-grub
/etc/kernel/postrm.d/initramfs-tools
/etc/kernel/header_postinst.d
/etc/kernel/header_postinst.d/nvidia-common.dpkg-remove
/etc/kernel/header_postinst.d/dkms
/etc/kernel/prerm.d
/etc/kernel/prerm.d/dkms

rgrep rpm /etc/kernel
->no result

One interesting result: in the package dpkg the following files contain the string 'rpm':
/usr/sbin/dkms
/usr/lib/dkms/common.postinst
/usr/share/doc/dkms/examples/sample-suse-9-mkkmp.spec
/usr/share/doc/dkms/AUTHORS
/etc/bash_completion.d/dkms

and /var/log/apt/term.log contains the following lines which were called during this time:
run-parts: executing /etc/kernel/prerm.d/dkms 3.2.0-26-generic /boot/vmlinuz-3.2.0-26-generic
run-parts: executing /etc/kernel/prerm.d/dkms 3.2.0-27-generic /boot/vmlinuz-3.2.0-27-generic
run-parts: executing /etc/kernel/prerm.d/dkms 3.2.0-31-generic /boot/vmlinuz-3.2.0-31-generic
run-parts: executing /etc/kernel/postinst.d/dkms 3.2.0-39-generic /boot/vmlinuz-3.2.0-39-generic
run-parts: executing /etc/kernel/header_postinst.d/dkms 3.2.0-39-generic /boot/vmlinuz-3.2.0-39-generic

replaying these commands (again, now on raring instead of precise), don't create a /.rpmdb but a /root/.rpmdb. So again, I assume, this happens because in apt-get/dpkg, the commands are called with a reduced set of environment variables, and then this directory is created. in fact, I assume $HOME is not set:

# ls -ld .rpmdb* /.rpmdb*
# HOME= /etc/kernel/postinst.d/dkms 3.8.0-14-generic /boot/vmlinuz-3.8.0-14-generic
# ls -ld .rpmdb* /.rpmdb*
drwxr-xr-x 2 root root 4096 Mär 24 13:02 /.rpmdb