It will work. Typing this on a computer running 2 different sets of DDR2 800 (2x1GB Elpida and 2x2GB A-Data). Working just fine and has been for a while now. Did something similar with my old C2Q 9550 machine, had 2 different OCZ kits running fine. The only tid bit of advice to help ensure stability is to run the slower kit in the slot 1 and 3. Then the faster stuff in slot 2 and 4.
Here's a screenshot of my mismatched RAM in CPU-Z.