Michael/Toby

We never got a specific reason, but many possible theories:

Toby is the only person in the office that doesn't have to listen to Michael, since Toby is technically from corporate.
Being that he's the HR rep, he is the one who has to squash many of Michaels ideas.
He's just so low energy and boring that it drives Michael nuts.
Toby had a family and a daughter, but got divorced. Michael is desperate to have a family of his own and is jealous that someone like Toby could have one, and lose it.

I always thought it was pretty clear it was because Toby was a wet blanket to Michael's shenanigans and the only one who could say no. Michael disliked Holly when he first met her for precisely that reason. He also had some negative feelings towards corporate itself. He doesn't like authority figures if they stop him form having fun.

I think everyone is on the money here on this one because if you remember, in season 9, Andy hates Toby too.

It's a running joke on the show that every office hates their HR rep. Michael hates Toby, and Holly at first. When Jim was briefly put in charge he started to get irritated by Toby, then yelled at him when he was co-manager. Andy starts to hate Toby when he's in charge. Even David Wallace bemoans his HR guy during Jim's interview.