Let's monitor the processes. Install htop.
Start htop. alt+f2, type "htop". Or write "htop" in terminal.
sudo apt-get install htop
Press f6 (sort by). Select cpu%
When it starts to get sluggish, monitor the cpu%. Look at top of the list. Write down the text under "command". Read the cpu %.
What made my netbook get sluggish was apport. A system report tool to send info to Ubuntu. As much as I would like to contribute, it was locking up my system everytime it was running in the background.
In case it is the same for you:
change the value 1 to 0
sudo gedit /etc/default/apport
You can notice the change after rebooting or by typing in
Information at http://askubuntu.com/questions/93457...disable-apport
sudo service apport stop
edit: Just realized your not using a netbook like me. This observation is probably not what you are experiencing then.