It depends, some are in start-->programs-->"start/launch/whatever..."
The rest is in the register: Start-->run-->"regedit.exe"
hkey_local_machine/-->software-->microsoft-->windows-->current_version-->Run (Some malicious programs are sometimes hidden in 'RunOnce' and 'RunOneEx'. If you changed your config and you choose to restart later, there may be some good stuf in these too, so reboot your before you check them.)
Search in hkey_local_user and hkey_users-->default too.
Right click the item you want to remove, and choose delete. If you don't know if a key is usefull, right click and edit (modify?) it, and add rem and a space at the begining, the line will be ignored by windows, and you can still re-enable it if needed.