How long is a piece of string?
Most bus fares in Thailand are under 500 baht, meaning even a 20% commission is only US$2-3. I've never even tried to book ahead, as I've never had a problem just showing up and getting on the next bus.
For train tickets, which are a far more limited resource (at least for sleepers etc) and can't be booked online (curse you, SRT!), around 200 baht plus credit card surcharges is typical. (2017 update: online bookings are back, although only for limited destinations.)
For airplane tickets, commissions are usually built into the price, the agent is highly unlikely to tell you how much but around 5% from the airline is typical. Commissions are a form of competition, so agents will push the airlines with the highest margins, and they may well add some extra margin on top! If you're booking straightforward point-to-point or return flights, you'll avoid all the commissions and get the best prices by booking online.