i have run into this problem in Intrepid.

It came after a video editing tool caused my system to crash or forced me to reboot.

any application started from the command line returns:
(firefox:6804): GnomeUI-WARNING **: While connecting to session manager:
None of the authentication protocols specified are supported.

list of problems I noticed so far:
gone are nautilus bookmarks
gone are firefox bookmarks
can not restore bookmarks from (the .json formats) the bookmark manager  in firefox
can not export bookmarks into html in firefox through bookmark manager
can not create new bookmarks in firefox
no updates are made to browsing history which means I
can not go back and forth through browsed pages
can not save files from browser to computer (save prompt does not appear)
starting Azureus (now called VUZE) returns this error: 
Save of 'azureus.config' fails
No space left on device
details:
     java.io.IOException: No space left on device
	at java.io.FileOutputStream.writeBytes(Native Method)
	at java.io.FileOutputStream.write(FileOutputStream.java:260)
	at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
	at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
	at org.gudy.azureus2.core3.util.FileUtil.writeResilientFile(FileUtil.java:453)
	at org.gudy.azureus2.core3.util.FileUtil.writeResilientFile(FileUtil.java:429)
	at org.gudy.azureus2.core3.util.FileUtil.writeResilientFile(FileUtil.java:408)
	at org.gudy.azureus2.core3.util.FileUtil.writeResilientConfigFile(FileUtil.java:390)
	at org.gudy.azureus2.core3.config.impl.ConfigurationManager.save(ConfigurationManager.java:233)
	at org.gudy.azureus2.core3.config.impl.ConfigurationManager.save(ConfigurationManager.java:268)
	at org.gudy.azureus2.core3.config.COConfigurationManager.save(COConfigurationManager.java:371)
	at org.gudy.azureus2.core3.util.AEDiagnostics.markDirty(AEDiagnostics.java:460)
	at com.aelitis.azureus.core.impl.AzureusCoreImpl.<init>(AzureusCoreImpl.java:169)
	at com.aelitis.azureus.core.impl.AzureusCoreImpl.create(AzureusCoreImpl.java:102)
	at com.aelitis.azureus.core.AzureusCoreFactory.create(AzureusCoreFactory.java:46)
	at org.gudy.azureus2.ui.swt.Main.<init>(Main.java:80)
	at org.gudy.azureus2.ui.swt.Main.main(Main.java:216)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.gudy.azureus2.ui.common.Main.directLaunch(Main.java:229)
	at org.gudy.azureus2.ui.common.Main.main(Main.java:132)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at com.aelitis.azureus.launcher.MainExecutor$1.run(MainExecutor.java:37)
	at java.lang.Thread.run(Thread.java:619)

Azureus(Vuze) seems to be perpetually scanning for something. This is indicated by the progress bar at the bottom that keeps is stalled in mid progress. That section is usually used to keep track of update files for the Vuze app. Vuze still works.
Vuze will also continually report that it can not save anything to the drive as it seems full.

can not start pidgin
gedit returns this error when trying to save a file: 
     There is not enough disk space to save the file. Please free some disk space and try again.
there is enough space, i know this for a fact.
system monitor is fully functional but confirms the false error and tells me (in the "System" section):
      Available disk space: 0 bytes
this is also confirmed in teh "File Systems" section.

other apps tested:
world of warcraft through wine version 1.1.3
evolution mail
skype
compiz

other applications confirmed to start up correctly but no further testing was made:
kino
pitivi video editor


I don't see how this qualifies as a "low" ranking.