The X9650 by a marginal increase in performance but compatibility depends on your motherboard's TDP support. The Q9650 is a 95W and the X9650 is 130W so your motherboard may not support it... it's also a lot more expensive. The original price was near $1000.00 US but by now who knows.
Sorry: I meant the Intel Core2 Quad Q9550 @ 2.83GHz vs Q9650 3.0Ghz
Either would be good, the 9650 is around 4% faster than the 9550 but may be more expensive... the 9550 (2008) has a newer version the 9550S (2009) that's a 65W TDP.
The Q9650 was originally priced about twice as the Q9550 but by now their price difference may be a few tenths of dollars.