So besides the built in ones here is a basic list of the modules I used. I had use some of the in non-intuitive ways, and others I had to really change the way they looked.
CCK
Flag
Pathologic
Automatic Nodetitles
Global Redirect
MimeDetect
Node Comment
Path redirect
Pathauto
Quick Tabs
RPX
Token
Panels
Rules
User Karma
Wysiwyg
Views
Voting API
Vote Up/Down