From http://usesthis.com/.

 

IDE

Komodo - mainly for python

Visual Studio - c#, c, c++

Intellij Idea - java

Eclipse - too slow and bloated

 

Collaborative Text Editing

Etherpad

Google Wave

 

Text Editing

TextMate

vim

 

Reading and Bookmarks

Bloglines, Google Reader

Instapaper

del.icio.us

Xmarks

 

Email Clients

Thunderbird

GMail

Outlook Express - Not kidding. It was fast, streamlined, and compatible with everything. Now it is deprecated.

 

File Transfer

Winscp

 

Tracking

Gutata - notes and thoughts (of course!)

Wakoopa - tracks software use

Todolist - todos and notes

Evernote - notes

 

Special circumstances

No internet

 

Portability

Synchronization

Subversion and TortoiseSVN - version control and file storage

Dropbox - store and synchronize files remotely