Check out Techspot's PC buying guides
to get a general idea of what's in store these days - they're fairly recent (June 27) and cover budget, mid and high end configs.
A 2001 rig definitely calls for an upgrade but installing Windows fresh with just what you need would give the system quite a boost. Also, there's no safer time to overclock, if your system permits it, than when you're looking out for a new system.
Just repeating the advice I was given in a similar thread, consider going in for two smaller HDDs - you can get better performance by putting them in a RAID, even if you don't implement RAID you can be more secure mirroring important data to another physical disk. I found WD's (7200 r.p.m) drives to be slightly slower than Seagate, but cheaper too - and they have the same warranty period.
Fans - I'd guess this would depend to an extent on how hot your video card runs, the newer multi-core CPUs run quite cool, just make sure you have a front fan blowing straight at the HDD/s as f0dder has suggested in more than one thread. My case came with two small ones already installed at the side so look out for something like that. My suggestion, get a BIG case - they're airier and can save you a lot of trouble later if things start getting cramped.
Audio card - Wish I could answer this one conclusively coz I need to decide the same thing for myself. ATM, I have got the onboard audio (Realtek) hooked into a Sony component system and with Foobar's kernel streaming support the sound is _crystal clear_, kind of a damper really... I was looking forward to getting the Xonar Lashiec suggested! But, never say die!
I assume you aren't considering Vista since you're not looking for a very high end rig, still... just in case... DON'T!