The price difference between a system based on 754 3400+ and a system based on 939 3500+ is very little, and almost 0% in total cost. So
between the two, IMO, I would narrow down to a 939 system at this point. The 939 has better cover for high memory bandwidth applications (such as video encoding/streaming, scientific) and longer lasting 939 compatibility.
Further from this poll (2 days old), less than 10% (3 out of 38 voters at this time) of the voters would settle for a 754 system for good, meaning most people would want a 939 eventually. If one builds a 754 now, there will be resale and possbile loss when replacing 754 with 939 later.
http://www.ocforums.com/showthread.php?t=315646
For choice of motherboards (both 754, 939), please refer to these two posts which link to lots of reviews, anandtech editor choice and some members experience.
For 939, MSI K8N Neo2, ABIT AV8, Gigabyte K8NSNXP-939 ($200+), ASUS A8V (new version maybe) are possible choice.
For 754, EPOX 8KDA3(+/J), MSI K8N Neo, ABIT KV8, Gigabit K8NSNXP are poplular. Some boards can support mobile A64.
A64 Nforce3 Motherboards (754, 939) (post 11)
A64 K8T800 Pro Motherboards (754, 939) (post 12)
Exemplary A64 systems: setups, results and experiences (post 63)
For memory modules for A64, this post discusses many aspect for A64 memory and lists many modules, including tradeoff among them, e.g. tight timing under 250 MHz or relax timing for 250-300 MHz.
Memory modules (for 754 and 939 platforms) (post 14)
I suppose video card and graphic card in your list mean the same thing.
If targeting for PCI-e, there is no motherboard until later 2004 to run PCI-e video card, such as motherboards with Nforce4 chipset.
For price-performance, a 9800 pro 128 MB can be had for under $200.
For latest high end card for gaming, X800pro 256 MB is very poplular.
For power supply used for overclocking, the popluar choices are
Antec True Power (480W, 550W), Fortron (530 W), some Enermax. Antec TP 550 has higher 12V current rating and fan control. Haven't follow lately whether there are some good new ones.
For HD, WD with 8 MB cache are very inexpensive now. Let other to comment on some new Raptors. Most Nforce3 boards have native chipset support for RAID 0/1/0+1/JBOD.