With Intel you have three choices-
- Obsolete Socket 755 boards, which are
well supported, have excellent
performance for their price but the
new C2D/C2Q processors are getting
less available and more pricey.
- Socket 1156 boards, which
do not have well supported on board
video, and have somewhat pricey
- Very pricey Socket 1366 systems.
than the Socket 1156 on board video
issue, compatibility on Intel based
boards is excellent.
With AMD, you have a broad range of low cost dual, three and quad core processors at every possible price point up to the quad core Phenom II 965BE, which is roughly the same performance as a Core 2 Q9550 quad-core or some of the middle-end Core i3/i5 processors. AMD is coming out with a new Hexa Core soon that will be supported by most AM2+ and AM3 motherboards with later chipsets. All modern Phenom II and Athlon II processor work equally well on AM2+ and AM3 motherboards, the only difference being which memory you buy for the M/B, DDR2 or DDR3. I would recommend avoiding any AM2 (non- "+") motherboards/CPU's (unless someone gives it to you) as it may limit your upgrade path.
I just purchased a Gigabyte GA-MA785GMT-UD2H, Phenom II 550 X2 Black Edition, and Corsair DDR3/1333 memory solely for Linux use. I moved Ubuntu 9.10 over to it, did a single dpkg-reconfig xorg-xserver and had mpg/avi/flash video and working OpenGL. Ethernet and Sound worked immediately with zero effort. I haven't put FGLRX on it yet but may wait until 10.4 comes up and just upgrade. I just unlocked both cores and ran Prime95 for a half hour with zero errors, so it looks like I have something close to a Phenom II 955BE for half the cost.
I got an AM3 board because no matter what, I had to purchase memory for it, and I figured buying DDR3 was more future proof than buying more DDR2. There is little to no performance difference between DDR2 and DDR3 due to the higher latencies of DDR3, so if price/performance alone is the issue DDR2 is not a bad choice.
While AMD/ATI has angered a lot of folks with older video cards by dropping driver support, they have made great strides in supporting their newer cards under Linux in both the open source and proprietary drivers.