OK, here is how I find out some of the stuff running at startup. As soon as you boot, log into windows as fast as you can, then fire up Task Manager immediately. Go to the Processes tab and click on the CPU label - twice I think, to sort by CPU usage descending. Now any process that's using CPU will be at the top of the list. Watch Task Manager for a few minutes and see what's running - it's a little tricky 'cause a lot of services are starting, but you might be able to spot a real hog or something that you don't want running at startup. I go through and google each thing I don't recognize and find out what it is.
Some of the things are a judgment call - a lot of antivirus programs will do anything from a quick scan of the boot sector and registry up to the whole windows directory or even more - *that* can take a while and it grinds on the disk, but it protects you at least a little. Or a lot of things stick themselves in there to check for updates. Oh make sure you're not running 2 different resident anti-virus programs, that will CRUSH your performance.
The next step up from eyeballing what's running is to get lists of what's running at startup, HijackThis from Trend Micro is pretty good (but has some learning curve), I think SpyBot Search&Destroy had a fairly decent one, and SuperAntiSpyware too iirc. Argh I just looked at mine, I see AVG (the antivirus I've been running) has been installing more and more stuff at startup - maybe time to switch again, each antivirus seems to go through sucky periods where it's more annoying than helpful
Since it looks like something's hitting the disk hard from the way you describe it, the next thing to do is to configure Task Manager to show disk usage stats and then sort on those. Depending on which version of Windows you have, it will probably be something under "Options" or "View" like "Select Columns" - Page Fault Delta, I/O Reads, I/O Writes can be interesting to look at, watch your startup sorting on each of those columns and see if something looks like it's doing a suspiciously large amount of work...