Your library would be the most likely source of "phantom" stuff, and if it's three gigs that's probably where all the new data is.
A lot of stuff is stored in your Library folder; your email would be the first thing I'd check--3 gigs is a lot, but if you get a lot of attachments or have a huge backlog, then that's possibly the source. This can, I think, be moved to another partition, but I've never done it myself.
The other two parts of the library to look at are "Application Support", which stores "extra" data for various apps and may be bloated with something unnecessary (don't just haphazardly chuck all this, though, or it might break some apps), and "Caches" which does just what it sounds like. The stuff in caches can usually be junked (and can definitely be tossed if there's a cache for a program you don't use anymore), but be careful you don't delete something important.
You could also try downloading Tiger Cache Cleaner and see if running the maintenance routines, tossing old log files, and maybe clearing some basic caches frees you up some space.