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 Profile/Google Maps, Remember The Milk as to do list.

SNS
Twitter and FriendFeed, I am not a big fan of Facebook.

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)

QuickGold (iPhone) Petit Launch (Palm OS)

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.

Firefox (Cross Platform)
Firexox Extension List: Firefox on Linux    Firefox on Windows

Thunderbird  (Cross Platform)
Nearly perfect email client.
Recommended extensions: Thunderbird on Linux    Thunderbird on Windows

Dropbox (Linux/Mac/Windows)
Cross platform file synchronization tool. 2GB+ space for free to get all your files stored and synced in the cloud. You should give it a go. Otherwise you will regret some day.

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:)

Adium (Mac) Pidgin (Windows/Linux)
Nimbuzz/Fring (iPhone)
All-in-one IM client. MSN/Gtalk/Yahoo/AOL/QQ/Jabber/XMPP/ICQ/IRC/SILC/Sametime... Whatever u can think of.

Emesene (perfect MSN Client for Linux and Windows, fuck Windows Live Messenger!)

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.

Backup Tools
iBackup/Silverkeeper/SuperDuper!/CCC/rsync/Timemachine/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)
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.
Client
PuTTY for Linux and Windows
Terminal.app or iSSH.app for Mac OS X
How to encrypt your network communications via SSH Tunnel?
How to fuck GFW?
Please check the article here: SSH Tunnels

Input Method (Chinese)
Linux iBus + ibus-pinyin (scim + pinyin is not very good)
Mac OS X IMKQIM/QIM (shareware) FIT (freeware)
Windows 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)
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)
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 (Mac/Linux/Win)
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.

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 PAC/DAT script 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