Yeah, chipsets, BIOS, everything has to be ready for Core 2 Duo. Also the new nVidia supports Core 2 Duo.
To add another wrinkle, not all boards that do support Core 2 Duo will support the EE editions, like the quad processor, so if you plan on upgrading the CPU & not the MB in the future check for that.
But you don't really have to wonder too much. Any MB that supports the Core 2 Duo is going to be bragging about it in big letters on the box. "Subtlety" not being in the MB manufacturers dictionary (except when it comes to support, then they're all about nuance as they don't help you.). So "subtle" is tech support's dictionary, but not marketing's.
If you're upgrading from a "somewhat" old system to the Core 2 Duo (somewhat being about 12 months nowadays) make sure your PS supports the new ATX v2.2 specification that has that 8 pin connector. Some PS don't have it at all, some have it natively, and others make you cobble together 2 4 pins to come up with the eight.
ATI chipsets will let you use CrossFire, very stable and good boards.
Intel chipsets will let you use CrossFire too and generally are the most stable boards
NVIDIA chipsets will let you use SLI and the last 680i boards have reported to be very very good boards
VIA chipsets, dont really know, I dont use them. I cant say anything about them.
Now if you mean the differences between 965, 975x, 680i, RD600 etc. There are not too many differences, you will almost find the same features on most of them. Main difference will be support for either Crossfire or SLI. The rest is almost the same.