I'd go with the new Intel line of CPUs. They are affordable and much more powerful than any AMD out on the market. Just compare the benchmarks located on several websites. Most of them show a bottom line Intel Core 2 Duo outperforming some of the higher end AMD cpus.
Matter of fact I can confirm this because I just received my new PC last week.
I have the mid range E6600 2.4 Core 2 Duo processor(s) and 2GB of DDR2 RAM @ 800Mhz and this system rocks!!! It boots up fast and games boot even faster. It takes just a few seconds (maybe 10 seconds) for me to load a new patrol compared to my old 3.2HT Intel Pentium 4 with 1GB of PC3200 RAM @ 433Mhz used to take me almost 2-3 minutes to load a new patrol. Not only that the new processors used a lot less power consumption and aren't nearly as hot inside the case which keeps your PC from heat damage and sluggish game performance.
I haven't seen a slow down in SHIII since getting this baby and even with the GW mod and zooming in on heavily burning ships in a large convoy I am still getting solid 60FPS or more. I have it sync'd so it tends to lock at 60FPS which is fast enough and totally smooth. The only time the FPS drops is when I used Time Compression at x4096 it drops down to 10FPS. At x2048 it runs at 20FPS. <---That's what I used to get in heavy ports in x1 normal compression.
There are some cheap motherboards that support PCI-E graphics and the new Core Duo 2 processors and the new DDR2 RAM @ 800Mhz. Your are looking at spending maybe $100 American dollars just for the Motherboard.
The processor I am using is roughly $400-$700 depending on where you buy it from. Some companies are ripping people off out there unfortunately.
There are other processors below mine that are still faster than most AMD chips out right now and those Intel chips are roughly $150 - $399.
The RAM I am using is roughly $150 per every 1GB module. I am using 2 modules so therefore my cost for RAM was $300 roughly
I am using the Nvidia 7900GT 512MB GPU. It is a nice card with fast GDDR3 RAM. It cost me about $350 for this card. The 7900GTX version was nearly double that and I found that to be a bit high for an extra 5FPS in some shooter games.
Honestly I would stay away from AMD for awhile and go with Intel. Until AMD comes out with a new design again that puts Intel to shame. Which won't probably be for another 2 years or so.