As it is today:
Athlon FX: 1 MB cache, dual channel (144 bit) memory controller, socket 940 chip, requires registered RAM like servers/workstations ((slightly more expensive, slightly slower, better stability). Basically, Athlon FX is nothing else than the fastest Opteron 1xx.
Athlon 64: 1 MB cache, single channel memory controller, socket 754 chip, does not require registered RAM.
The FX is only available in a single speedgrade which equals or bests the fastest A64 (and opteron). Its aimed at people with money to burn (like those considering P4 Extreme Editions), as it is barely faster than the (fastest) A64's, yet quite a bit more expensive, requires more expensive motherboards and more expensive RAM. The upsides are you get the best performance available today, a slightly better upgrade path (you'll be able to stick even a dual core Opteron in your motherboard next year), and an unlocked multiplier (easier/better oveclocking). If you want value for your money however, I would avoid it.
In a month or two, both A64 and AFX will move to socket 939, both will sport dual channel memory controller, neither will require registered ram, but the FX will still have 1 MB cache, while the A64 will see its cache cut in half (to 512 Kb). As a result, AFX will get slightly faster than today (no more registered ram), A64 will gain on some apps (dual channel), lose on some (smaller cache), but overall probably perform slightly better than todays A64's.
In short: get a A64. You could wait for S939 if you're really not in a hurry, but a slightly better upgrade path is hardly a reason IMHO to wait two months. By the time you'll want to upgrade beyond a 3700+ (fastest cpu on S754) you'll want a new motherboard anyhow.
= The views stated herein are my personal views, and not necessarily the views of my wife. =