Ahh, how to mess with botters.
First, always always always always report them. Target the character, right-click their character portrait and choose Report for Cheating. Blizzard uses this information to study new bots and kill them all at once in large waves, though don't be terribly surprised if the bot disappears in a day or so; that does happen occasionally as well.
Second, as was already suggested in a comment, kill them (on PvP servers or in battlegrounds). Bots aren't terribly smart, so they're not very good at combat; they typically have a preprogramed rotation that runs much slower than the GCD or cast times of the abilities being used, and cannot adapt to changing circumstances. Sometimes bots run naked or with broken armor. During Cataclysm, when I was spending a lot of time playing on a PvP server, I was routinely killing level 85 bots at level 80-81. If you have a lot of time on your hands, you can camp the bot at the graveyard, or even round up a whole bunch of bots there.
Another option, which even works on PvE servers, is to compete with them head-on. Bots typically follow a set route and don't deviate from it, so you can actually arrive at a resource node ahead of the bot, herb or mine it, and confuse the bot. Sometimes this can cause a poorly written bot to crash.
If you see that a bot is in a guild, make an effort to contact the GM or an officer of that guild. This is a strong indication that the account is compromised and the guild should take steps to lock down its access or temporarily remove it from the guild. They (and the real account owner) will thank you for it...unless it's a botting guild! If that happens, well, open a ticket. The GMs will love to hear about a guild dedicated to botting. If you suspect the account is compromised, be sure to note this in the text field when you report the player for cheating, or better yet open a GM ticket.
Finally, a note about reporting bots: When you report a bot for cheating, you'll get a text field where you can enter in an explanation. Don't just put in "botting" or anything like that. Instead, describe the specific unusual behaviors that the character engaged in, e.g. running in a circle or making too-perfect direction changes, always casting the same spell over and over even when it's inappropriate, or whatever other behavior you noticed.