I just purchased an AMD Phenom 9850BE and was wondering what architecture I should use? Should I use the AMD64 Architecture or stick to the x86 architecture? I haven't had any experience with a 64bit Linux system or quad cores before so any feedback/experience with what architecture I should use would be greatly appreciated. (I am most likely going to install Debian, also the system has 4GB of DDR2 1066)

Use AMD64 also known as x86_64.

x86_64 runs both 64bit and 32bit code and can be 25-70+% faster on AMD CPUs than if the CPU was running in 32bit mode.

GL

Thanks! That's what I figured I should install but I wasn't sure if there were any known problems with the 64bit version of it and not liking certain cpus. Thanks again!

I suppose the only thing that you need to be careful of with 64-bit CPU support with a known-to-be 64-bit desktop processor is that you get the x86_64/amd64 version and not the IA64 (Itanium), ppc64, SPARC64, or MIPS64 version. I haven't heard or seen of any cases where x86_64-capable processors wouldn't run an x86_64 distribution but I have heard of several cases of people trying to use IA64 install discs with Athlon 64s and P4s/Core 2s and they wouldn't work. I've also seen people try to boot 32-bit chips with a 64-bit install disc and that doesn't work either. Most of the people that I know that did that have a P4 Prescott 5x0 or an early socket 754 Sempron that are one revision ahead of the chips with the 64-bit parts unlocked. Well, there are a few that are little farther off, like my brother who tried to install a Vista x86_64 beta on his P4 Northwood unit as he thought that Pentium 4s were all 64-bit, not just some of the later ones.

Drivers... ATI GPU...
that's the only issue I have came across...
most other software (specially open source) already come 64bit

^ 64-bit stuff comes faster on open source... anyone found a 64bit working Flash for Firefox?

No, it does not exist yet. Try using nspluginviewer to wrap the 32-bit executable so 64-bit browsers can use it.