Your SB-600 is already compatible with Nikon's CLS wireless (infrared) flash control system. It's a pretty good system to build around; you get TTL (ie: automatic exposure), multiple flash capability, and remote control of your flash level. I own one of these flashes myself, and it's definitely a nice option to have.
Unfortunately, your current D3000 body doesn't support CLS. (My D90 does, as does any of the bodies you mention in your upgrade plans). You can buy an add-on adapter (Nikon SU-800)(http://www.nikonusa.com/Nikon-Products/Product/Flashes/4794/SU-800-Wireless-Speedlight-Commander.html) that will act as a "Commander" for your CLS-enabled flash.
I personally wouldn't spend money on it, depending on how soon you plan to upgrade. CLS is nice, but there are downsides:
- Nikon-only. You generally can't use 3rd-party flashes with it.
- Preflashes. The flash flickers a couple of times before the actual exposure happens. This introduces a delay, can potentially trigger blinks in people, and can interfere with optical triggers (which other posters have discussed).
- Need line-of-sight, which won't work in all lighting situations.
If these aren't a big deal to you, then you might want to build around a CLS system. If that's true, and you want to go off-camera right away, and you don't mind spending some extra money, then the SU-800 is a great way to start. Note that it will be compatible with your new body. It'll be unnecessary (since those cameras use the built-in pop-up flash as a CLS commander), but still useful (you get extra control options on the standalone commander unit).