Ok, I'll try to do my best here.
Intel core2 Quads are usually overpowered for most gamers needs. Therefore it matters not which one you choose they will both perform similarly in games. At the very least, the difference between the two would not be worth $100.
The other side of that coin is Overclocking, and with that comes the synthetic benchmarks. The Q9400, while a respectable chip, cannot overclock as high as a Q9550 or Q9650. This is because the Q9550 and Q9650 have a higher multiplier than the Q9400.
So, the choice in the end is yours:
Gaming/ General use = Q9400
Overclocking/ benchmark glory = Q9550 (or i7

)