Bonds may have been tested for steroids and the other substances in the MLB drug testing program - but he was not tested for the components that are in The Clear, The Cream and/or HGH. These are designer steroids for which there are no current tests and/or not tested under MLB's program.
That Barry didn't test positive for a "base" or "standard" steroid does not mean he is automatically clean. In reality, outside of Raffy (who is his own enigma), the players who have tested positive are mainly role players w/o the big bucks to afford the higher end stuff. As such, I have honestly not been surprised at the lack of big names/numbers of steroid violators. When you're making $5M+, why risk using the cheap stuff you know they are testing for when you can afford the expensive stuff they aren't testing for?
Bonds allegedly used a clear substance and a cream. Where they steroids or flax seed oil? Only Barry and the people at BALCO know for sure. But, that doesn't mean he's clean (or not clean). All the negative tests show is that if he did use anything, he wasn't stupid enough (ala Raffy) to use something that was being tested for or could be tested for.
The MLB drug test plan was a lot of pomp that, in my opinion, accomplished little at cleaning up the game. Until they start testing for HGH and the higher end steroids, all they'll do is stop the little guy from using the basic stuff - which is at least a start.
As for his return, it will be interesting to see how he does. If he was juiced before, and is truly clean now (no HGH, etc.), he should show a drop in performance. If he has always been clean, then nothing should change and he should be back to his 1.400 OPS self. Either way, here's guessing he gets walked in his first AB if he comes to the plate with anybody on base.