Some of my favorite tools

Development

C++, Perl I have an irrational dislike for Java. I am ashamed of this but there, I said it.
Git - source control Linus Torvalds developed it. Ergo, I use it or something less fanboy-ish.
Vim - text editor Once you get past its near vertical learning curve, beats any IDE hands down.
Mediawiki - wiki I haven't really tried out other wiki software. Works well enough.

Mendeley - to organize academic papers I used Zotero for a while but I had to ditch Firefox and Zotero doesn't have a Chrome version. Mendeley's social features while rudimentary are a definite plus.
Skim - to annotate and view PDFs Scribble on the sides of all the papers you read without devastating yet another swathe of forests. Best of all, it's free!

Remember the Milk - todo list manager By far, the best online todo manager.
Evernote My digital brain.
Mint - personal finance tracking The only sane way to manage passwords. It's pen source and has mobile apps.
Mint - personal finance tracking Provides a consolidated view and does decent analysis.
Dropbox - online backups Other competing services are Mozy and Carbonite. Dropbox won in this category because 1. it offers access to your files via the web 2. offers versioning (albeit limited to the last 30 days if you are too cheap to spring for its paid service.)
Google Calendar
Google Reader - RSS aggregator

Kindle I absolutely love it to bits. Wish it did a better job at rendering research papers though.
Android powered Nexus S I for one welcome my Google overlords. They own my data, ergo they own me. I foolishly am fine with that.