And that is why, ideally, you don't rely on a single partition. Reformatting Windows becomes so routine that losing all of one's precious shit ceases to be a problem if you store it all on something other than C:\. You know, as long as the drive itself doesn't die. But that's why you then use a combination of optical media for backups and maybe even a second hard drive. Still though, multiple partitions FTW.
As to the original problem, the "thinking light" is the HD access light (it'd be awesome to have a front gauge for CPU usage tho) and heavy HD access on startup is unsurprising for most Windows systems, especially those that haven't been reformatted in a while. My suggestions there are to defrag the drive, and either remove some things from startup, or just remove some things altogether. Even with 1GB of RAM (which is pretty much standard these days) HD thrashing will still occur, especially if you're loading a lot of stuff, and killing explorer.exe won't help because Windows Explorer doubles as the Windows shell.
I also suggest replacing Task Manager with SysInternals Process Explorer (it's free), since Process Explorer is a much better tool for figuring out what could be causing a bottleneck in performance.
EDIT: Or just use this to figure out wtf is causing the HD thrashing on startup.
i said it DOESN'T do anything after it logs on - it just sits there, saying that windows is doing some really insanely powerful.
i actually use process explorer. it still just lists explorer as automatically going up to 100% CPU load within a minute of it loading. i thought for sure it's gotta be some sort of virus because it never really did that in the past, and i'm only loading some five small applications on startup. i never run more than 44 processes at a time, according to the sysinternal tool, and only six of them are non-essential files.
i ran that autoruns thing, and didn't notice anything strange in there. would you mind taking a look at it and telling me what you think of it?