whats the bottleneck in my system?
Asus M4A79XTD evo
PhenomII 550be - 3 cores @ 3.1GHz
Asus (two red fans) 4890
Kingston 2x2gb DDR3 @ 1600MHz
Samsung F3 1TB
Win7 Pro 64bit
Frankly, I wouldn't do anything right now. You can stick in a USB 3/SATA III card later when the ports are actually useful. You could upgrade to a 5xxx series card, but you've got a powerful one already. Wait until it's too weak to game and then buy a new DirectX 11 card.
I would expect that your current motherboard would support new processors with a BIOS update, so moving to 890 would be one of the last things I would recommend. Of course, it will depend, but you're unlikely to see any performance improvement with a new mobo.
The biggest true bottleneck that I see is your hard drive. Getting an SSD would make the biggest non-gaming difference to your system, though it's pricey. The biggest gaming bottleneck is, as MadAdmiral said, the GPU. Upgrading to an ATI 5870, 5970, or an nVidia 480 is about your only option, though. Well, or buying another 4890 & crossfire, if your mobo & PSU will support it.