Botnet mining is absolutely going to be a problem. As many have pointed out already, a large botnet could take 50% of market share almost overnight. Imagine a botnet of 1 million PC's (quite common), the cpu's running at half intensity would absolutely destroy profitability for "honest" miners. Now lets imagine that 10% of these computers have descent GPU's or that just 1% have some of the top of the line ATI GPU's. You can now see the problem. BTW The idea that botnet operators would have to choose between running, say a spam network and a bitcoin mining operation is false, what is to stop them doing both? The incentive's for these guys are enormous. Bitcoin mining over the botnet paradigm provides a direct route to quick cash.

There are however, some technical problems for the botnet operators to overcome, e.g. collecting the mined coins, preventing user detection.... but i can't see anything that won't be solved by clever code. Can we as a community come up with some method to prevent this from happening? Almost certainly not unless we can find a way to force some kind of user interaction into the mining process. I can't imagine how? Would we could at least do is ask the pools to come up with some security measures to prevent obvious use of botnets in their systems, but that would be require an incentive to do so, whilst yet right now they will be earning lot's of fee's by ignoring the problem.

Will bitcoin become associated with hackers looking for cheap bucks? I think so. Maybe we can persuade the big exchanges, the community and the pools to watch out for botnet behaviour (it should be fairly obvious) and thus attempt to make it difficult for these guys to cash out easily. Perhaps in the end the backbone of the bitcoin mining network will be controlled by botnet's, it may be an inevitability we have to accept.