Some usuful troubleshooting commands I've found are: (all in an X-term shell)

dmesg

This lists out the last 100 or so kenel messages

top

This gives a constantly updating screen of top most CPU hogging processes.

apt-get update

This is the same as refresh in the aplication manager, but give usuful messages about its status

apt-get -f install

This will find and try to fix any packages that did not install correctly. This includes ones you might not know about.

apt-get upgrade

This is also the same as in the application manager but will give more information about what did and did not upgrade

The are lots of other apt-get as well as dpkg program options that can solve various problems once identified.

Hope this helps.