What OS are you using? You'll need a 64-bit OS to fully use 4GB+ of RAM. A 2x2GB setup would work best so that your RAM runs in dual-channel mode. I would just keep your existing motherboard and CPU and get new RAM.
I was just wondering whether to get 6gb of DDR2 ram or to wait and get a new motherboard with DDR3 memory?
It depends on what your current PC specs are or if you need a new second PC Desktop? What OS are you planning to run on that 6gb configuration because the 32bit versions of XP, and Vista only need 3.5GB max. If you are planning to run Windows 7 then its ok. Will you need that much RAM, not currently, like I said it all depends on what your MB, GPU, CPU, and OS are, as well as what software you will be using that can utilize that amount of RAM.
If I were you, I would wait for the true next gen PC desktop systems with USB3.0, cheaper SSD's, BD drive, and Windows7sp1, perhaps hexacore or even newer core i7's w 32nm. Then Id build a DDR3 based system and max it out.