First off, you are better sticking to FS9 with the new CPU than FSX, you will probably get better results.
Anyway, with regards to your question, you have not stated which Opteron you are looking at, so that is hard to answer, but the Toledo core 4200 X2 is a good S939 CPU. I had one, and it worked flawlessly for quite a while before I upgraded - I don't think you'd be disappointed with it.
As Ivan said, S939 CPU's are rare now, best bet is probably eBay. This site has it in stock in the UK at a very reasonable price:
http://www.yoyotech.co.uk/product_info. ... ts_id=4720NOTE - That cpu is OEM - processor only, no fan/heatsink.
With regards to BenF23's question, FSX supports dual core (with SP1 - not sure about before this). Therefore, a dual core with a slower core speed will easily outperform a faster single core. It's simple maths really

e.g. 1x 2.6Ghz = 2.6Ghz
2x 2.2Ghx = 4.4Ghz
Simple

Without knowing exactly what opteron you are looking at imchief, it is hard to give a full answer to your question, but as I stated before, the Toledo is a good CPU. As Ivan mentioned, it is "cache crippled" (L2 = 2x512Kb - Total 1Mb).
If you are looking to run FSX well, and any future PC games, you really want to upgrade to AM2 (Or Intel - they way outperform AMD at the moment). Also, this would allow you to upgrade to DDR2 RAM (much better in gaming - DDR2 speeds start where DDR speeds end). A decent motherboard, cpu and RAM upgrade can be got for a fair price these days, so I would advise that.
With your system, even with the new RAM and CPU, you will probably get better results with FS9.
Hope I've helped

If anything needs explaining, drop by and PM me, I'll be happy to help

Regards,
celtman