My philosophy of choosing software: Simple, free, open source, cross platform. If not, cost effective.
Web apps
Gmail/Google Reader/Google Calendar/Google Docs/Google Talk/Google Profile/Google Maps, Remember The Milk as to do list.
Google Apps
SNS
Twitter and
FriendFeed, I am not a big fan of Facebook.
Twitter Client (Official Web recommended)
Chromed Bird (Chrome extension) good!
Hotot for Chrome (cross platform)
Echofon for Firefox
Echofon for Mac (best twitter client on Mac!)
Tweetie for MacHotot (Linux)
Pino (Linux)
TweetDeck (Adobe AIR)
HootSuite (Web UI)
@Mobile (iPhone)
Tweetie (Twitter for iPhone)
TweetList
TwitBird/TwitBird Pre
Echofon
Rescue Kit, your Swiss Army Knife;-)
BackTrack 3/4 (You know what it is, right?)
System Rescue CD (based on Gentoo Linux)
GParted/Parted Magic
CloneZilla (Open Source Norton Ghost equivalent)
Knoppix (based on Debian)
App Launcher
Quick Silver (Mac) Google Quick Search Box (Mac)
Gnome Do (Linux/GNOME) Launchy (Windows/Linux)
Executor FARR Find and Run Robot (Windows)
Superb app launcher on Mac/Linux/Windows. I can't live without those launchers even for a single day. Besides Launchy, Executor and Find and Run Robot are good alternatives on Windows.
Search (file and folder locator)
Everything
Locate files and folders instantly!
Firefox (All platforms)
Firexox Extension List:
Chrome (All platforms)
Extensions:
Thunderbird (Cross Platform)
Nearly perfect email client.
Recommended extensions:
Dropbox (Linux/Mac/Windows) 
My referral link (both of us will get 250MB extra space)
Cross
platform file synchronization tool, one place for everything if you have too many computers and synchronizing files become a headache. Free 2GB+ space, get all your
files stored and synced in the cloud. Give it a shot!
Remember The Milk (Web Service/iPhone app)
Online GTD tool, service. Keep your to do list everywhere. Provides the ability to integrate with Gcal. Kicks ass!
Evernote (Mac/Windows/Linux/iPhone) Office OneNote 2007 (Windows)
Evernote
is the excellent notebook service solution (Best I have ever seen), on
Mac/Windows/Linux/Web/Mobile, all in one and it is always kept
synchronized. Another good part of it is the iPhone app, use snapshot notes, come one! You can't miss it!
Onenote is not bad for Windows users, especially when you need team collaboration. Well you need to pay for it (I guess most of you guys don't). Import
Onenote notes to Evernote and u can uninstall damn Microsoft thing:)
IM: Adium (Mac) Pidgin (Windows/Linux)
Emesene (Linux/Mac/Windows) Probably the best 3rd party MSN client, fuck Windows Live Messenger!
Nimbuzz/Fring (iPhone)
All-in-one IM client. MSN/Gtalk/Yahoo/AOL/QQ/Jabber/XMPP/ICQ/IRC/SILC/Sametime... Whatever u can think of.
Meebo (Web apps)
Web based multi protocol IM solution. Give it a go when u r on someone else's computer and want a chat.
Cygwin (Windows)
Linux like environment for Windows. I am so addicted to Linux commands.
Dexpot/VirtuaWin/Desktops/Virtual Desktop Manage (Win)
Workspace,
virtual window manager. I can't bear with a stupid single desktop
design for Windows. So I use VirtualWin and Desktops from Sysinternals.
However, no need to do that on Linux or Mac. It's amazing to use hot
keys to switch workspaces. Apple 'stole' Workspace from
GNOME/KDE/XFCE/CDE/JDE (or other desktop environment I am not familiar with)
and make it even better in Leopard.
Clipboard Manager
Mac OS X
ClipMenu (freeware) Clips (shareware, bought via MacHeist bundle)
Linux
Parcellite (GTK+)
Windows
Ditto (freeware)
Backup Tools
iBackup/Silverkeeper/SuperDuper!/CCC/rsync/Time Machine/Mozy (Mac OS X)
Microsoft SyncToy 2.0 Syncback (Freeware)
Back in Time (Linux)
rsync and its front-ends, grsync/gadmin-rsync
Desktop Virtualization
VMware Workstation (Linux/Windows)
VMware Fusion (Mac)
Oracle VM VirtualBox (Sun VirtualBox) Free, open source acquired by Sun, now acquired again by Oracle! (Linux/Mac/Windows)
Not yet stabilized, it is still a toy rather than a reliable tool for daily work.
Parallel Desktop (Mac)
VMware Server Freeware (Linux/Windows)
SSH
Server
Linux and Mac OS X OpenSSH server
Windows CopSSH or winsshd.
Client
PuTTY for Linux and Windows
PieTTY
Terminal.app, iTerm.app (iterm2), iSSH.app for Mac OS X
JellyfiSSH (SSH host bookmark manager)
How to encrypt your network communications via SSH Tunnel?
How to fuck GFW?
Please check the article here: SSH Tunnels
Fonts
Windows/Linux DejaVu Fonts DejaVe Sans Microsoft YaHei
Mac OS X... NOT necessary...
Input Method (Chinese)
Linux
iBus + ibus-pinyin + ibus-sunpinyin2 (scim + pinyin is not very good)
Mac OS X
SunPinyin for MacOS 2.0 (freeware) IMKQIM/QIM (shareware) FIT (freeware)
Windows
Google IME
Sogou Input Method
Mindjet MindManager (Mac/Windows) FreeMind/Xmind (Mac/Windows/Linux)
Dump your mind, GTD(Get Things Done) tool.
Hamachi (Mac/Linux/Windows)
LogMeIn Hamachi is a flexible VPN service that enables anyone to easily
connect multiple internet-enabled computers into their own secure
virtual network. This is the ultimate solution to manage multiple computers at home and office. Wonderful!
Windows Live Folder Share (Windows)
Remote file sharing and access, works like .mac (MobileMe).
Windows Live Writer (Windows) MacJournal (Mac OS X, paid apps)
Blogging client, the best ever blog client tool I have ever seen. I can't believe it is from Microsoft Windows live team, and it's FREE. Remember to
download a copy of Windows Live Writer backup to backup settings,
drafts and entries if you don't want to do it manually like me. It's
free, I still believe that Microsoft can deliver good stuff as long as they want.
Windows Live Mail (Windows)
Wonderful mail client from Windows Live pack. Perfect support for hotmail/live/msn account. Try this if you don't like Gmail and Thunderbird
SMPlayer (Linux/Windows)
QT front-end for mplayer
VLC (Mac/Windows/Linux)
Kmplayer (Windows only, listed in the hall of shame by ffmpeg)
mplayer (Linux)
mplayer OS X extended (Mac OS X)
Movist (Mac)
MPlayerX (Mac)
Splayer (Windows)
The new ultimate media player solution for Windows.
Screenshot
Linux
scrot (CLI), Shutter (formerly Gscrot)
Mac OS X
OS X built-in (cmd+shift+3, cmd+shift+4, cmd+shift+4+space = window), Instantshot!/Skitch/Dashboard Widget
Windows: PicPick/EPSnap (freeware) Snagit/HyperSnap (Shareware)
Take Screenshots on the fly.
TrueCrypt (Cross platform)
Cross platform open source Encryption tool to secure all your important data. Strongly recommend, it works exactly the same under Linux/Mac/Windows, OMG!
Keepass (Windows) KeepassX (Mac/Linux)
Keep your passwords safe in KeePass. *NIX OS please use KeepassX.
FTP/SFTP Client
Filezilla (FTP + SFTP) (Mac/Linux/Windows)
Cool
open source project, rated as best FTP client on Lifehacker. And now
it's cross platform, which is fantastic. What's more, it supports SFTP
(SSH File Transfer Protocol), perfect equivalent for WinSCP under all
OS.
Cyberduck (Mac)
Free FTP Client on Mac. The icon is cute and my wife likes it. Also supports SCP.
Flow (Mac shareware)
FlashFXP (Windows)
I
paid for this shareware because I have been using it since 2000. It's
life time upgrade and support. The author is a good guy. FlashFXP is
the best FTP client I have ever seen on Windows. And I keep all my site
info there. There is a tool to convert site files between
FlashFXP/Filezilla/CyberDuck. FlashFXP supports Site To Site FXP.
WinSCP (Windows)
SCP client for windows only. Probably the best choice if you run Windows and transfer files to a *NIX host via SCP/SFTP. Of course you can run in WINE, but not sure if it works 100%.
Sysinternals suite (Windows)
Powerful tools for Windows users.
Office Suite
OpenOffice.org (Windows/Linux) NeoOffice (Mac)
Free Office Suite, cross platform. Kick the shit out of Microsoft Office.
iWork '09
It's commercial software, normally bundled with your Mac. But I think most of the users are willing to pay for it. Most of the time.
Skype (Mac/Linux/Windows/iPhone)
Most
popular VOIP client on any OS. Chat with your buddies with AES
encryption and free PC to PC call, as well as cheap PC to phone
international calls.
Note: Skype for iPhone works over 3G/GPRS once you jailbreak and install VoIPover3g package.
CDBurnerXP (Windows) ImgBurn (Windows)
Embrace freeware, abandon chunky Nero.
K3b (KDE Burn Baby Burn)
Famous CD/DVD burning software for Linux, KDE. Can be used under any DE/WM, as long as you installed the dependencies.
HFS (HTTP File Sever) (Windows) Runnable via WINE on Linux.
Woof (UNIX/Linux) Simply exchange file with this Python script.
SIP Client
X-Lite (Mac/Linux/Windows)
XAMPP (all platform)
Portable Apache httpd, MySQL, PHP, Perl combo, easy to install and uninstall. Available on Linux, Mac OS X and Windows, bingo for testing, debugging and troubleshooting!
P2P
Transmission (Mac/Linux) with WEB UI
μTorrent (Windows/Mac)
aMule (Mac/Linux) with WEB UI
emule (Windows)
rtorrent (Linux/Mac)
mldonkey (Linux/Mac)
Media Center
XBMC
Photography:
GIMP (Linux/Mac)
Paint.NET (Windows)
Photoshop (commercial software) available on Mac/Windows, runnable on WINE under Linux.
PicPick (Windows)
QQ (Mac/Linux/iPhone/PalmOS) TM2009 (Windows)
Sometimes
file transfer and remote assistance via QQ/TM is perfect. MSN sucks!!!
I also like the file sharing/hosting in QQ mail, 1G per file and you
can keep it as long as you like. I have to say, it's good! Tencent is
getting bigger and more internationalized.
As we all know, QQ is not a safe IM tool to use. So avoid using it whenever possible.
Note: Skype and
Messenger for Mac does not understand the proxy script PAC/DAT file.
For Skype we have to specify the http proxy manually in system prefs.
Messenger for Mac just doesn't work behind a proxy, idiot! SHIT! Messenger for Mac 7.0.2 fixed the proxy bug.
To be continued...
More useful links: Links