A list comparing windows and linux applications:  http://wiki.linuxquestions.org/wiki/Linux_software_equivalent_to_Windows_software

The following is a list of applications I use on my Ubuntu 10.04 machine that enable me to replace my windows machine.

Bandwidth Management and Proxy
Squid

Graphics
Gimp
PDF Editor
Xsane Image Scanner

Office
Efax -gtk
glabels label designer – cd and dvd labels, bussiness cards etc
planner – like MS Project
Kivio – like Visio
Open Office

Internet
aMule – peer to peer
Azureus – Torrents
Downloader for X – Download manager
gFTP – ftp client

FileZilla

KPPP – internet access
Skype
Firefox

Programming
Amay – web editor
kompozer - web editor
electric – electric cad system
kicad - Electronic schematic and PCB design software
klogic - digital circuit editor and simulator for KDE

Sound and Video
Audacious – mp3's like winamp
Audio cd extractor
k3b – cd and dvd writer
ManDVD - tool for generating video DVDs – including still images
Sound Converter
Tvtime
vlc – All movies
Totem Movie Player – DVD's, DVD ISO's

Media Server
http://mediatomb.cc/
MediaTomb is also compatible with your PS3 (Thanks to Ir33 for informing us about this nice app)

There is another application PS3 media server that works pretty good.

Windows emulator
wine

Games
Chromium - fast paced, arcade-style, scrolling space shooter
foobillard
Scorched 3D - A 3D Remake Of Scorched Earth (available in repositories)
Torcs - car simulator (available in repositories)
Vdrift - open source drifting simulator(not in repositories) - http://vdrift.net

Encryption

For folder and file encryption use:

encfs (Integrates file system encryption into the UNIX file system)

Cryptkeeper (This is a encfs tray applet)

Accessories
gdesklets
Blue Tooth File Sharing
For mathematical, electrical, mechanical, physics, astronomy, biology, biophysics, earth science,
econometrics, statistics, medicine and all kind of other applications be sure to visit:
https://help.ubuntu.com/community/UbuntuScience