I always called Magus Janus because I feel that, after the climatic events in 600AD, he sheds the Magus persona and, to a certain extent, reverts to the person who was Janus. Sort of like how Anikan Skywalker became Darth Vader, and then, briefly, reverted back to the person who is Anikan Skywalker. Then he died. But that's beside the point!
Besides, in the Star Wars: Infinities series he survives and joins the Rebellion, taking on an all-white version of the suit to take on Palpatine and the Galactic Empire...
As for Frog, I've always called him Glenn. Well, maybe not always, seeing as how I didn't know Frog's real name was Glenn my first playthrough... I also went through a period where I called Robo "Iron".