Depends on the purpose of the computer. This is what I will do on my typical gaming rig:
1. Windows 7, 64bit edition
2. Updated Desktop drivers
3. Update Windows 7
4. Install GPU drivers
then to ensure everything is as it should be the following tools:
1. Speedfan (or any other temp monitor program)
2. CPU-Z
3. GPU-Z
4. Crystal Disk Info
5. Cyrstal Disk Mark
6. HWM Blackbox (if I feel like it)
7. PC Wizard
8. IO Meter
9. 3dMark 06
10. 3dMark Vantage
11. 3dMark 03
12. 3dMark 11
13. Prime95
When I am satisfied that everything as above runs as it should, I will delete it all barring 3dMark06, Crystal Disk and the temp monitor of choice. (I rerun 3dMark06 with driver updates, Crystal disk to see the performance on SSD (mine doesn't support trim) and temp monitor when my pc is acting up.
Then I will start with the tools
1. 7Zip
2. Alchohol 120
3. UltraEdit
4. Firefox
5. VLC
6. Diskkeeper
7. Fraps
Then the programs
1. CS5
2. Skype
3. Steam
4. MS Office (maybe depending on how I feel)
5. ITunes
What I will NEVER install on my gaming rig is the following:
1. XFire
2. Anti-virus
3. Firewalls
4. Spyware
5. Widgets