Thought I'd pipe in on this, as having a team with 120 wins in a season gets me suspected of this (naturally).
I agree if you think your commish is cheating, just leave. Two of my owners seem to think it without having any real proof, but they refuse to leave. They'd rather stay and just be a pain in the ass.
Anyway, things I try to do...
I don't trade with new guys. If I feel I MUST... I'll ask 5 or 6 different people in the league (whoever is online at the time) if it's a fair deal for the other team to ensure i'm not screwing them over.
In things like Free Agency or Coaching bids or whatever, I make sure I stop bidding at least 12 hours or so before I end bidding so I can't just "sneak" a bid in.
I lose. Over and over.
Okay, this isn't on purpose but having a team that wins 120 games might be a sign that cheating goes on, but to have that team constantly bounced out of the playoffs is a good sign against it... and absolutely maddenning for me.
Bug in OOTP?
The problem with leagues like mine (talent only) is you REALLY have to trust the commish, because they can cheat and go unnoticed. That's why I don't understand why the two who think I'm cheating stay in the league. Regardless, there's evidence against this at times (the contract I signed Barry Zito to... ugh.)
It all comes down to trust, really. If you don't trust your commissioner, it's likely not to be fun and you should just leave. Ultimately, it's a rare case when you can be certain that a commish is cheating, but there have been some good methods mentioned to check for it. I encourage you that if you do think your commish is cheating, not to make a big scene out of it though. Simply leave... make up some reason. I know it pisses me off to hear people even suggest I'm cheating simply cause of the amount of work I put into the league, and to hear that just bothers me, as I assume it would other commissioners. But if your slight suspicion turns into something that you can't just ignore... you have to leave.