Ultimately you get much better metering, and hence, pleasing results, when you use Nikon flashes with Nikon DSLRs. The TTL system is a God-send, honestly. Your "success rate" is much higher with Nikon Speedlights.
This alone should be reason enough to spend that little bit extra for them.
ON TOP OF THAT, D90 + SB600/SB800 gives you the benefit of advanced wireless lighting (part of Nikon's CLS). So... I don't see what more you can ask for.
I just got a 2nd hand SB600 for $230 from fellow clubsnapper. Really happy with it.
$200+ for new 3rd party flash, vs $200+ for great condition 2nd-hand SB600. The choice is clear.
D90 is quite fussy over third party flash. My D90 does not work with metz in TTL mode(cannot meter, cannot fire the shot although it can focus). I have to set it to M to get flash fire.
but the same flash(Metz) does work at D200(my friend's camera). I read in internet, D90 is not compatible with some third party flash. I am thinking to get SB600 when I can save enough. I can use it as slave also (like one bro suggested above)
If you are really going for a third party flash i would say the Nissin Di622 or the sunpak PZ42X. Both have mounts for nikon or canon, and from what i see Di622 is very easy to operate. Just on the flash,once the ready light is on you can fire away. There is auto focus, power 1:1 to 1:34(if i got the numbers correct) and it works with nikon I-TTL system,do check out some reviews about it. As for the sunpak PZ42X there is a LCD screen which you can tune your EV adjustments on it,but slightly less powerful than the Nissin. Nissin's guide number is 44 at ISO 100.