This took awhile to think about, but I think I have a couple. First of all, Pleinair from the Disgaea games. She's just a NPC, but I dunno, she makes my inner fanboyism come out. Plus, in the manga (which is only one of three I read, btw), she's pretty funny.
Another one Arche. Talk about fanboyism. xD I absolutely loved her in Tales of Phantasia, probably the liveliest character in the bunch. He hair is just a big bowl of fun, she rides on a broom, she has an awesome, funny personalty, and a complete masacre on the battlefield. Sooooooo... ya. Really, really, love her a lot, on my top five list most likely.
I guess I can but Lyner Baresett from Ar Tonelico up on here. Wow, what a character. =D This kid was SO ignorant lol. Out of his group, there was his love interest, and a girl who kinda liked him. And he acted like a complete idiot. Really, it's not even funny how good they made this guy so clueless. There was one point in the game, where ther girl who liked him, Misha, had to sing to keep to keep the bad guy at bay. So, Lyner goes and says somethin like, "Misha, can you sing to keep _____ in the tower?" Not those exact words, but something like it. So that means she would have to stay in the same place for the rest of her life, or most of it, and sing that song. Then Misha runs away, and he's like "Misha?". Then girl he likes, Aurica, says "Lyner!", and he's like "What? What did I do wrong?". See what I'm saying? That's just a sample. This guys not stupid, he's just clueless, and konws NOTHING about girls. The dialogue in this game is really funny, and Lyner adds to it. He's also a fucking powerhouse, and has a cool Voice actor. Funny, ignorant, but cool person.
Junpei from Persona 3. Man, this guy is fucking hilarious... he makes the funniest jokes in this game, seriously. For most of the game, he's a fucking clown. He's barely ever that serious. All around, a fun-loving, awesome guy.
Naoto, from PErsona 4. She has a great character. Her awkwardness towards her gender, her horrible social skills, and her amazing ability to make breakthroughs in investigations... all just a part of who she is. She also has a good social link. <3