Formal:
* Certainly
* Indeed
* Absolutely
* Of course
* By all means
* Without a doubt
* Affirmative
* I agree
* You bet
Informal:
* Yep
* Yup
* Sure
* Right
* Okay
* Alright
* Definitely
* No problem
* You got it
* Roger that (mainly used in communication)
More specific:
* I will (for agreement to do something)
* I understand (for agreement to a statement)
* That's right (for confirmation)
You can also use a gesture like nodding your head to indicate agreement.
The best way to choose an alternative to "yes" depends on the context and how formal the situation is.