Secunia just makes a list of all your installed programs, then looks at possible revisions.
Windows, Your Antivirus, Flash player, Adobe Reader, and Java are the critical ones as far as overall security.
Compiling your data is what takes a while during the first one or two times it runs.
You don't HAVE to get Works updates via Secunia. You can get them directly from Microsoft.
It doesn't MAKE you install Winamp. You can do what you want. If you want it to ignore Winamp, you can change the settings to do so.