I think some little kids have called Satoshi and Kasumi that, though I could be wrong.
Kojiro, Musashi, and Nyasu don't use honorifics 'cause they're close, like Satoshi-tachi.
But they use '-sama' in reference to Sakaki 'cause he's their boss (when they refer to him by name- now they tend to just say boss.)
-chan's used for younger characters, girls, and pets. Harley using it on Musashi's... pretty weird considering she's probably older than him.
Musashi-tachi called him Harley-sensei in the alliance episodes (and even after in Kojiro's case, though he just says sensei. He can't seem to be able to remember his name. He's always either calling him Ariados-tsuki/Noctus-tsukai or sensei or something even vaguer. xD
Harley calls everybody and everything (his Pokemon plus his food) except for Senri, whom he he calls Senri-sama, and Shuu, who is Shuu-kun.
These Wikipedia articles are pretty helpful with their meanings:
http://en.wikipedia.org/wiki/Japanese_suffixes
http://en.wikipedia.org/wiki/Japanese_titles
>>>Although traditionally honorifics are not applied to oneself, some young women occasionally develop the habit of referring to themselves in the third person using chan.
Miyamoto does that. She calls herself Miyamoto-chan. xD
The old couple in the Manene episode called Kojiro something ending in -chama if I remember correctly.
Mondo calls Kojiro and Musashi senpai too, methinks. Though, depite Wiki saying it's used only for boys, I've seen plenty of girls in anime refered to as kun. xD
Faiyaa Kojiro (Moltres James!) refered to himself as ore-sama. xD