The Opteron dual cores, 165, 170, and 175 all have 2x1MB of L2 Cache, while the X2s all have 2x512KB of L2 Cache, except for the X2 4400+ and X2 4800+ having 2x1MB of cache. The Opterons also run at a lower stock vcore, which means more headroom and lower temps. The Opterons have been seen to be able to OC better then the X2s, most Opterons go up to around 2.7-2.9ghz, while X2s top out at 2.6-2.7ghz.
If you can afford the dual core, the Opteron 165 starts at around $300 or so, then definitely go for it. The X2 3800+ is around $280, so definitely opt for the 165.
What about memory compatibility? Do the Opterons work with standard DDR memory? I assume that you can use just about any 939 socket mobo with the Opterons, no?
I had been toying with getting an x2 4200+ but the 1 mb L2 cache per core looks like a definite advantage. I'm also very interested in keeping the system as cool as possible with as little noise as possible. Overclocking is not a very high priority for me. Also, it appears that you can't get OEM versions of the x2's but you can certainly get them for the Opterons. Since I plan to get an XP-120 + fan for cooling, I'd just as soon get an OEM package.