1) It will be very hard to wrong with an intel board coupled with an intel processor. There are almost no over-clock features, but that results in some of the most rock solid systems available.
2) As long as you stay away from VIA chip sets, it will be very hard to go wrong with an AMD processor and motherboard set (ASUS makes a very good mobo to support the AMD cpu). An ASUS mobo and amd cpu is a great combination, IMHO.
3) Linux supports borth cpu types.
4) Currently (and I sress currently) intel cpu's perform insignificantly better where video pre-processing is concerned (cad, etc.). Intel is better at this than amd, but not so's you'd notice. AMD cpu's, on the other hand, have insignificantly greater throughput; they can be slightly faster than intel, but again not so's you'd notice.
5) Of greater concern is the over-all health of the companies. Unless AMD's new 64-bit processor is a hit, and remains so against a 64-bit intel cpu, AMD is likely to be relegated to a niche market, if that.
6) I own and use both processors, and I have no particular preference.
7) I own oodles of intel stock.