Two ways to say yes (or more?)
What's the difference between hai and ee? :)
はい hai: yes (polite)
ええ ee: yes (polite, colloquial)
うん un: yeah (not polite, colloquial)
そう sou: yes, like that
And sometimes, remember that Hai doesn't necessarily mean 'Yes'. Sometimes, it means 'I heard what you said, and I may not agree but want to at least acknowledge that I heard what you said.'
Same applies to ええ or うん. It's a foible of Japanese pragmatics that when someone is explaining something taking a paragraph or more, you are supposed to encourage the speaker by saying some form of "yes" every 1-2 sentences or so.
This said, in most situations, periodic grunts usually suffice to keep a conversation moving along smoothly (especially if you are a foreigner).