Memory leaks are a fairly common problem in some games. How much RAM are you running and do you reboot to help free up RAM before playing? Also what size page file do you use and is the drive defragged?
I actually disable all fetching except for boot fetching to help keep more free RAM available. Some have argued the need to do that, but in my findings W7's fetching is a RAM hog.
We did a test on my friend's rig and after disabling all but boot fetching, the lag he was getting in Crysis cleared up. I was also shocked at how little difference there is in launching apps with it disabled, esp considering how much RAM is sucks up.
Note that there is also a very good defragging tool that's Windows certified which defrags sys files on reboot, including the page file. It's called Perfect Disk.
I suspect the Black Mesa mod, or certain uploads of it being reported corrupt archives, are causing similar problems, and yes, as MailMan said, I have had the same issues with Skyrim. I've been able to clear up such problems with Black Mesa via a reboot and defrag.
Upon defragging, Black Mesa files were the ones most fragmented. Aside from memory leaks, some games are horrible at fragmenting files written to the file page. I suspect those with memory leaks typcally have that problem too.
Lots of people rave about HL having a very liberal save writing feature, being able to quick save wherever and whenever you want. Yeah well it also has a quirky audio stutter when loading saves, indicating maybe it's trying to store them too quickly and fragmented. Google for Black Mesa videos and you'll see what I mean, audio stutter when loading saves is common.
It's kinda a bitch that one should have to use a minimum of 8GB RAM largely to account for poor coding, but what can you do? I built my X58 based rig with 6GB, and often times I wish I'd waited for 1155 and gone with 8GB.
Game engines can vary so much in what they do well and what they do horribly. I think a lot of devs get so caught up in what they want their engines to do that they don't take enough time to do proper performance testing along the way, and when they do, it's often on a best case scenario system than most can't afford.