Not sure of anyone can help me - random pausing

Hmm... This is a really weird question, but I've been having random pausing while playing doom. Like, the entire game will freeze up for like half a second. Otherwise, it's very smooth. This is source-port independant, as well. I've tried GZDoom, Zdoom, Chocolate Doom, PRBoom... All with the same odd pausing. I think I've noticed it in other games, though it's not as dramatic as in Doom, partially because I don't expect to be having any framerate problems with Doom. I've tried shutting down unnecessary background processes, I've done virus scans, I've scanned for spyware, I've defragmented my hard drive, and I'm completely out of ideas at this point. It's not a major deal, I suppose, but it does detract from the enjoyment from playing Doom, especially on more intense levels where perfect timing is essential. Kinda hard to dodge a barrage of imp fireballs when the computer goes on vacation unexpectedly. *shrug* I just don't know what the heck is going on, and I don't think anyone will actually be able to help me, but I just thought I'd try this as some sort of last-ditch effort.

I had this exact issue once and it turned out to be because I had left a browser window open that was periodically reloading itself (Firefox is so stupid that it uses 100% cpu every time it does anything)

You said you've closed down all unnecessary background processes; are you sure you've closed them all? It could be anything: a last.fm plugin, some malware you don't know about, etc.

Or a problem with your sound/music settings. Check those.

I have nearly this exact same problem and checked all over the net for answers, and so far i've come up with none.

What's funny is when I play more demanding games, like Far Cry, Call of Duty, etc., I never get stuttering like I do in doom.

Considering I played Doom on a 386 with 33mhz of processing power for at least a year (that means low-res mode at about 4-6 frames per second), I've gotten used to the pauses and occassional slowdown of running it on a modern machine.