I thought some of these suggestions could prove to be useful if you didnt order the components yet...
CPU
I would first suggest getting Athlon 64 3400+ 2.4ghz 512kb socket 754 cpu instead for
$288
This cpu will be actually faster than the 3500+ which is only clocked at 2.2ghz and features the same 512kb cache but duel channel supposedly adds the increase in the speed rating. Of course in reality this only amounts to 3-4% maximum. Now going from 2.2 to 2.4 already gives you 9% increase and office apps as well as gaming respond better to increased mhz speed. Bottom line:
Faster performance at almost $100 less than 3500+ Since this chip comes at 2.4ghz, it should have more overclocking room as well if you need it.
MOTHERBOARD
This would imply going with a 754 socket motherboard, which are again cheaper.
Something for $80-100 should fit the bill.
Motherboard Roundup (socket 754)
If you dont need all the bells and whistles, Chaintech VNF3-250 board has everything from SATA, to 100LAN, and onboard audio, except firewire. It only costs
$75 and is an excellent board. This would save you another $50 on your motherboard purchase. Socket 754 and socket 939 boards both have the excellent nforce 3 250 chipset with a working agp/pci lock and perform identically besides the dual channel difference.
RAM
Since latency is not really important for A64, got with cheap PC3200 ram unless you intend to overclock (then go with PC3500 or higher). I recommend getting 1 gig. Maybe something like
Corsair Value 512mb PC3200 C2.5-3-3-8 - $79 x 2
This should save you more $$$ on more expensive RAM. You shouldn't get 512mb in 2 sticks of 256 now because then if you have to get 512 more you will use up both channels and have to use 2T memory timings, which have about 2-9% additional performance loss for a dual channel A64 (so you'll actually be even more slower than by going with 1 gig socket 754 platform) This is a minor issue if you are gonna get 1gig in the first place if you went with socket 939 however.
VIDEOCARD
Isnt AGP Pro another way of saying AGP 8x? Maybe I am wrong but it sounds like a marketing gimmick to sell AGP 8x boards back in the days claiming they are 2x as fast as agp 4x.
Anyways since you'd save at least $150 by going with socket 754, buyign a better videocard shouldn't be as hard on the wallet. I think you should get something DX9 compliant at least, so at least you could upgrade to Longhorn operating system in 2006/7 which will require DX9 videocard. I am not sure if you want AIW again or not but 5900xt is a good recommendation. However ATI cards are much faster in PS2.0 and are better with AA/AF enabled than the 5xxx series. This
9700 is $150, for 10% faster speed you can get
9700Pro for $173 and for an additional 10-15% performance you can get
MSI 9800Pro $193, which can be flashed into a 9800xt card (or overclocked). If you want AIW package,
9700AIW is $199.
9700/9700pro/9800pro/5900xt review - this is an old review but somewhat useful.
Fastest Cards of Summer 2004 - this is a more extensive, recent review (you can gauge the performance of the 9700Pro cards by looking at - 10-12% of 9800Pro's performance.
Bottom Line: I'd probably get 9700 card for $150 since you even said you dont care much about gaming performance and that card will last a long time. If you are gonna spend near $200, get 6800 like others said (ie. EVGA for $285 which comes with a copy of Far Cry)
NOTE: The reason why I think socket 754 is better is because 939 dual channel barely gives any performance advantage while being priced a lot less favourably. Since right now A64 doesnt support PCIe for videocards, chances are that next time you upgrade you'll have to replace the motherboard. Besides even if you dont ugrade the videocard by then, most likely with a new cpu you'll get a new motherboard. But that's my opinion...