As cryptocurrencies are fairly new, I expect to see something pop-up in the near future. Golem for instance; wonderful design, but since its decentralized theres no way to prevent the usage. I wouldnt be surprised to hear somewhere down the line the network was rented to crack hashes or some other form of high computation required attack. I can't say much about a "botnet" as i'm not entirely sure if code can be executed during computation.

It's safe to say these acts will be performed elsewhere if not readily usable on the blockchain.