Most mobos have a fan header for the NB. Both my GA-X48-DS4 and GA-X58-UD4D do. Maybe it's old tradition, maybe they put it there if you wanted to change out the sinks to one that accepts a fan. You don't need to concern yourself with it though, unless you want to bench with LN2 and shove 3V+ through it.
The Thermalright Venomous is considered the best. Those are the three best sinks available right now. Which one is best depends on the airflow pattern in the case, then fans on them, the die configuration on the processor, the socket height and pressure on the retention system, and the TIM you are using.
Thermalright Venomous-X in stock now... - Page 4 - XtremeSystems Forums
Although they don't appear much larger than other coolers, it's the way they are made that makes the difference. The solder jobs between the heatpipes and fins, the aluminum and copper alloys used, the lap job on the base, etc. They are about as good as you can get with aircooling. Any larger and they would snap the board in half due to weight.
Obviously, some 38mm thick 3000rpm San Aces or Ultra Kazes would be the best fan configuration on any of them, but you'd go deaf. Scythe Gentle Typhoons, Slipstreams, Enermax Magmas, or some good ol' Yate Loon High Speeds would be adequate for your needs. Buy the highest fan speed available and use a fan controller. Lamptron FC2, FC5. If you want to go with 38mm high pressure fans, San Ace 1011, Scythe Ultra Kaze, or a Panaflo offering. Recommend going with 2000rpm or 'medium' speed fans with these options, however. 38mm thick fans make a loud electronic whine when they are toned down due to the nature of their motors. Phenom II's are good overclockers, but I'm not sure if you will meet a board/chip limit or a temperature limit first when overclocking. If this was my everyday rig, I'd stay in the 25mm thick fan category to reduce noise as much as possible. You don't appreciate quiet fans on your main system until you've installed 5 Ultra Kazes on your radiators.
As far as where to get them, I've spent about $1500 through Performance-PCs.com, ... sleeve it and they will come
with zero issues. They usually have the lowest prices and largest stock of enthusiast parts.
Edit in response to your edit: All of the sinks I mentioned are compatible with AM3/AM2 but will need special mounts.
Just add on AMD bolt-through kit at the bottom for $7.50.