I would get a pentium 4 CPU compatible with 775i65G, with the 6600 GT. I am using a P4 630 in Win98 (HT disabled) / Windows XP and the performance is quite good.

On the audio side I had a good experience in DOS with the YMF 724 card, you get real OPL 3 sound.

My inclination for a dos/win98 machine is something single threaded, so of your available processors that leaves the Athlon 64. After that I generally prefer team green over team red for GPUs, and the 6000 series Geforce cards were just a fantastic generation. Athlon 64 plus a Geforce 6000 series card was just an obscenely dominate combination when it came out. It's just a classic configuration.

Unless you have a specific game that doesn't like a bit of hardware (you wont know till you hit it) I'd go with as fast as you can. This will matter more in XP then 98 though.
Win98 will simply ignore anything after the first core, XP will benefit though so this puts me recommending the
Socket 775/6600 combination

Video, Try the Geforce 6600GT as its the fastest and if no backwards compatibility issues with any 9x games then your all good, otherwise drop back to the FX5600.
The FX5600 is a bit slow decent for XP IMHO but 100% 98 compatible, so its up to you if you want to hold back XP for the few 98 titles that don't work or hold back XP.
The Radeon 9600 is in between the two Nvidia cards but has compatibility issues of it's own but if plays all your games fine then probably better then the 5600.

Sound, Easy the Live.
9x and XP both take advantage of EAX. DOS support is average but your better off playing dos games from within windows on this rig anyway.

Now if you drop the XP requirement I'd do it the other way round and go for the slowest as any of the CPU's is more then enough for 9x
AMD/Intel choose your poison.
FX5600 -Fine card for dos/Win9x
Yamaha YMF724F or Live! The Yamaha has nice MIDI and OPL the live has EAX