For $350 you can buy an Intel Core i5 750 or 760, motherboard, and RAM, and that should net you better performance than a Q9650.
Otherwise just invest in a cheaper Core 2 Quad like the
Q9505.
Q9550,
Q8400, or
Xeon X3330 (Core 2 Q9400). You might be able to find these cheaper somewhere besides newegg.
All current sockets, that you can get if you were to upgrade platforms, are basically dead. Socket 1156 (Core i3 and i5) and socket AM3 have basically seen their best days. You would, in a way, be upgrading from one "dead" socket to another. So I don't really think you need to worry about it. The Core 2 Quad processors still perform pretty well. Despite being more expensive, you wouldn't have to change motherboards and RAM.
If "dead" sockets were a priority for you, then waiting to pick up one of the cheaper Sandy Bridge processors along with a new board and RAM is the smartest option.
Although one option is to pick up an AMD Phenom II X4 955, 965, 970, or an X6 along with a compatible DDR2 motherboard. That should get you Q9550/Q9650 performance for a cheaper price than newegg's listings. If you're using applications that are threaded beyond four cores then perhaps getting an X6 processor would be more beneficial than getting a Q9650.
MSI AMD 790X board +
Phenom II X6 1090T would be more potent than a Q9650, and roughly the same price on newegg.