I'm experiencing the same problem, if not similar enough: suddenly, most
applications freeze for a couple of minutes and then unfreeze. dmesg
doesn't show any messages for the moment of the problem. My system is
fully updated. The PC is new, so I haven't run any previous version of
Ubuntu on it. Let me describe three instances of the problem.

Instance 1: Some applications froze. Mouse is NOT frozen, keyboard is
NOT frozen. System monitor app stopped updating. A terminal still
responds. I was trying to kill pulseaudio when gnome-terminal froze
after a tab completion, right after hitting tab but before the beep or
the actual completion occurred. Workspace switcher didn't freeze, some
applications repaint others don't. Found another terminal and hitting
tab froze it too. Eventually, my PC was unusable, and eventually,
applications unfroze.

I couldn't kill pulseaudio.

Instance 2: A terminal still responds, I tried attaching strace to the
pulseaudio process with no luck. top continued running. Pulseaudio was
taking a constant 3% of a CPU, which seem pretty high to me. I have
killed pulseaudio and the terminal froze. Eventually, they all unfroze.

I killed pulseaudio.

Instance 3: As I'm writing this (under Opera), my System Monitor applet
stopped updating. I have a bunch of Link Monitor applets too, and they
seem to be updating correctly. The workspace switcher (with 3D effects
diabled) is still working. It lasted about 30 seconds. I didn't try
other applications this time.

Now it is updating again.

System is Jaunty 64-bit, fully updated. Partitions: sda[1-5].

alvar...@alvarezp-ws:~$ lspci
00:00.0 Host bridge: Intel Corporation 4 Series Chipset DRAM Controller (rev 03)
00:01.0 PCI bridge: Intel Corporation 4 Series Chipset PCI Express Root Port 
(rev 03)
00:03.0 Communication controller: Intel Corporation 4 Series Chipset HECI 
Controller (rev 03)
00:03.2 IDE interface: Intel Corporation 4 Series Chipset PT IDER Controller 
(rev 03)
00:03.3 Serial controller: Intel Corporation 4 Series Chipset Serial KT 
Controller (rev 03)
00:19.0 Ethernet controller: Intel Corporation 82567LM-3 Gigabit Network 
Connection (rev 02)
00:1a.0 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB UHCI 
Controller #4 (rev 02)
00:1a.1 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB UHCI 
Controller #5 (rev 02)
00:1a.2 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB UHCI 
Controller #6 (rev 02)
00:1a.7 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB2 EHCI 
Controller #2 (rev 02)
00:1b.0 Audio device: Intel Corporation 82801JD/DO (ICH10 Family) HD Audio 
Controller (rev 02)
00:1d.0 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB UHCI 
Controller #1 (rev 02)
00:1d.1 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB UHCI 
Controller #2 (rev 02)
00:1d.2 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB UHCI 
Controller #3 (rev 02)
00:1d.7 USB Controller: Intel Corporation 82801JD/DO (ICH10 Family) USB2 EHCI 
Controller #1 (rev 02)
00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev a2)
00:1f.0 ISA bridge: Intel Corporation 82801JDO (ICH10DO) LPC Interface 
Controller (rev 02)
00:1f.2 SATA controller: Intel Corporation 82801JD/DO (ICH10 Family) SATA AHCI 
Controller (rev 02)
00:1f.3 SMBus: Intel Corporation 82801JD/DO (ICH10 Family) SMBus Controller 
(rev 02)
01:00.0 VGA compatible controller: ATI Technologies Inc Mobility Radeon HD 3470

alvar...@alvarezp-ws:~$ cat /proc/cpuinfo | egrep 'model name|processor'
processor       : 0
model name      : Intel(R) Core(TM)2 Quad CPU    Q9400  @ 2.66GHz
processor       : 1
model name      : Intel(R) Core(TM)2 Quad CPU    Q9400  @ 2.66GHz
processor       : 2
model name      : Intel(R) Core(TM)2 Quad CPU    Q9400  @ 2.66GHz
processor       : 3
model name      : Intel(R) Core(TM)2 Quad CPU    Q9400  @ 2.66GHz

alvar...@alvarezp-ws:~$ uname -a
Linux alvarezp-ws 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:58:03 UTC 2009 
x86_64 GNU/Linux

-- 
Annoying freeze of some apps (gnome-terminal, xchat, audacious..)
https://bugs.launchpad.net/bugs/376168
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