Make sure you're pc is defragged. The biggest problem I have with valve is the loong level loading. It is possible with the same level of graphics to have almost seamless level transitions.
While fragmentation does cause blocks of data to be, potentially, scattered, that is NOT going to increase load times significantly. The access time is not much longer.
Something that effects loading, specifically, is the processor, memory bandwidth (as well as size), and the bus.
Having a dual core processor over a single core will show massive improvements in loading time, making the transitions in something like HL2 (with relatively small areas to load) nearly seamless.
If you don't have enough memory, the game will page it on the disc. Which, if the page file were fragmented severely, that
is something that could slow down performance. That still doesn't require complete defragmentation of the drive. (If you want to, go ahead, my point is it's probably not the problem).
If something in HL is running then you get a BSOD screen (said that HL2 crashes the machine), then there's a very good chance that a driver is crashing as a result of something in DirectX. One of the only guaranteed ways to crash a Windows XP machine is to make a device driver terminate inappropriately. Windows has no recovery for such an event and assumes something random is happening and turns your computer off "for safety".
Earlier, I didn't actually read the entire post, I thought you had that old stuttering sound problem, but it seems you have a much larger one.
I'm starting to think now, you should check out your sound card drivers.
I just want to point out that these issues are not related to the source engine in any way. The source engine uses the directx api ... which in turn is being managed by the OS. An error can occur in DX and the OS will catch that and do something about it. All the game did was call a DX function ... like InitializeAudioStream(), or something and the audio stream failed and Windows flailed it arms about.
Blame people whom are responsible for things like this.
As far as missing files go ... re download the GCF cache. I know for a fact that there are intact ones on the Steam servers since I've played the games you're talking about recently with no issues.
This is a localized event and doesn't happen to the majority of people using the products.
However, if it isn't missing any data, then there's obviously some sort of issue going on, and if it is only localized to you (and a few other people), then there's a good chance that the common difference is the cause, which would be hardware drivers ... again.
You can check the Windows log to see if there's any information about system crashes or driver errors.
Blame it on Microsoft, God does.