I've been replacing Microsoft tools one by one lately... IE was replaced by firebird ages ago. Second went Outlook, replaced by thunderbird (and sunbird... sorta, I don't do much calendaring as a student). Then, I taught myself the Latex typesetting system to replace Word. For class, I started using Matlab... I'm starting to think that can replace Excel.
Trac looks interesting for project management. It combines wikis, a ticket management system and source code control. I recently installed subversion to keep track of assignments... pretty cool... I use TortoiseSVN, a windows shell extension, to check documents in/out of the subversion repository
Here's another one that's hard to explain, but that I really love. Basically, this tool (for firebird) allows you to edit others' webpages at will. Look here for some cool applications of the tool. Among others, I have the amazon2melvyl and google scholar monitor scripts installed.