Hmm. What I usually do to "clean" up is basically run one of the many maintenance apps around, such as
Onyx,
MacJanitor or
Yasu (Yasu is the one I use, but I've tried the other two before), to basically run the cron scripts, and to repair permissions, reset logs and optimize the system.
Then I go manually into, first my home folder's library, and search in certain folders, specifically the Application Support folder and the preferences folder, and basically look for any program that I had already deleted, and then just the delete the files or folder. When I first got my Powerbook I used to go into every single folder of my Library, just to see what's inside, to familiarize myself. Most of the time if the thing is something you don't recognize (not a program that you had deleted) you probably shouldn't touch it.
Then I move up to my computer's library folder (since I'm the administrator of my computer) and do the same thing (note there will be less things to delete, because most programs install themselves only in your home folder) and then finally, just pop into the library folder inside the System folder to take a look, there are almost never traces of programs there. Note that if you're unsure of your way around the Mac as yet, I suggest just going in and taking a look, instead of happy go lucky deleting files from the library folders, especially if it's your computer's one, and ESPECIALLY be careful of the library folder inside your system folder, that one mostly contain OS library files, you don't want to be fooling around there unless you're very certain of yourself.
To be honest, there really ISn't much to clean up on the Mac, I do this routine maybe once in three months, when I remember? My powerbook just feels cleaner after it, it doesn't necessarily speed up by quite a lot, mostly because the Mac OS is clever enough to clean itself up on a everyday basis, not like Windows which likes to leave ugly traces in the registry and stuff. On the mac it's usually as easy as deleting a file, not like plunging yourself into the registry deleting lines of code or something. So don't worry too much about cleaning up the files, I would try one of those maintenance apps though, for starters, or just repairing permissions would help tons.
Hope this helps...
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