Honorifics and which words you choose to use.
Boku and Watashi are both "I" or "Me" in a sentence structure, and while we're taught in 101 class that boku is rude and watashi is polite, watashi is also the female word. Which is why in Hana Kimi's first episode, when she's trying to pass off as a guy, she accidentally says watashi and has to run before the other girls catch her (she says 'watashi mo' meaning "me, too"). [Later in the live-action JP series, two of the guys are talking about how they know she's a girl and will not try to date/hit on her until she refers to herself as watashi once more.]
Japanese is weird, but I don't think it's as odd as Spain-Spanish.
Note: you can also tell how rude a guy is in an anime if he says: "ore mo" or "boku mo". Sometimes it's also a given of age. Younger kids will tend to say "ore", while teens who want to appear tough say "boku."