There are so many ways to say "You" in Japanese, I'll just have to link to another blogpost again as they've already done the work. Knowing these may erase a bit of confusion if you're watching Anime.
Check out this post at Nihonshock: Saying “You” in Japanese.
あなた Anata is the formal "you", it's also not used very much.
君 Kimi is mostly used informally toward females, notably girlfriends.
Here are informal/rude ones and the ones you will hear most in anime:
お前 omae - informal towards someone (considered by the speaker) of lower status, or towards a friend (no need to be overly polite).
and the following three are downright derogatory:
きさま （貴様) - kisama
てめえ （手前）- temee
己 - onore
These last four are often translated as insults even. For instance when someone has insulted or treated the speaker - or someone they care about - badly, "temee!" will often be translated as "you bastard..." instead of "you", it could also be considered "why you..."