If there's one thing that puts me off an application, it's when it unnecessarily inserts itself into the Windows startup process so that it can have its very own system tray icon from whence it can spam me with annoying messages. Obviously it makes sense for some applications to run on startup (for example, I want Windows Live Messenger to be running without me needing to manually start it each time). The problem is that there are multiple places where an application can register itself for execution on startup, and this makes it hard to retain control over which programs are granted such esteemed status.
Of course, I wouldn't be writing this entry unless Windows Vista had a solution! From the start menu search bar, type System Configuration, and click on the link that comes up. You'll be required to provide privilege elevation unless you've disabled UAC, and then you'll see the following utility:
As you can see from the above screenshot, the Startup tab enumerates all the applications that are set to run as startup, regardless of whether they are set in the registry (either per-machine or per-user), the user profile, or simply the startup folder in the Programs entry of the start menu. You can disable any or all of them; they'll still be listed there so that you can switch them on again if you need to.
I should note in passing that this tool also allows you to do some other pretty useful things, like editing your boot configuration database (no need to master arcane bcdedit commands any longer) or accessing a variety of other system tools and utilities. It's the power user's configuration tool of choice - go check it out!