I've seen nakama used in One Piece a lot, but I've learned tomodachi in my text book. Is there a different in usage?
仲間: People who share the same goal and work/struggle/fight together in a group or organization. They often can be your close friends, too, but that's not necessary. A person whom you personally dislike, or whom you don't even know, can sometimes be your 仲間. In One Piece it sounds dramatic because it's about people who share the same destiny, literally in the same boat. That won't happen often in real life. 仲間になってくれ means "Join us," but not "Be my (personal) friend."
友達: A friend. Something based on personal feelings of intimacy or affection. You don't have to do something special with your 友達. They can be someone you haven't met for a long time.
In addition to blutorange's link, there's also a discussion here. Since it is in Japanese, let me just roughly translate the last part, which gives dictionary definitions of each term:
Tomodachi - A person with whom one reciprocates trust, and treats as an equal. Someone close that one hangs out with and chats with.
Nakama (first 3 entries)
- a relationship of doing things together, or such a person
- people of the same occupation, status, etc
- things of the same kind/category
It's a question of degree. 友達 is pretty much anyone you hang out with on a regular basis; 仲間 is a much closer relationship, almost like 'someone you choose to share your life with'. 仲間 also seems to have a sense of 'doing things together' or 'working towards a common goal' which is absent from 友達.
The context of shounen manga gives a nice demonstration of one boundary between the two. The protagonist's 仲間 are in effect the other main characters - the people that travel with him and work together with him to do whatever it is he's doing. His 友達 are all the other people he knows and likes - the ones that he'll hang out with if he comes across them, but they're not constantly with him and they're off doing their own things.
It's a distinction English doesn't make, so it's hard to think about when you're not used to it.