Here are a few for you;
Sou desuka? (is that so?) - sou kka!
Sou desu (that's right) - sou ne/sou da ne/sou da/sou sou
(variation of above, "sou yo ne" - means, "oh, I know"/"tell me about it")
Ii desu (it's good) - ii na!/ii ne!
Daijoubu (it's alright) - ii yo (usually said if someone is asking to borrow something from you or if they have your permission to do something)
Hai (yes) - un (the u is pronounced like the oo sound in spoon, but shorter, almost a mumble)
Nan dake - (what was it...) when trying to remember something
Chigau - (wait/that's wrong...) when you make a mistake and have to correct yourself
Ore? - (huh?/what the?)
Nan desuka (what is it?) - nan de?/nani?
Side note: ne is a feminine sound so men say it rarely, it's like saying "hey".