I've always wanted mahou shounen to be a subgenre, equivalent to mahou shoujo. Thing is, there is stuff like Sentai (so think Power Rangers), but I think that's totally different. I could think of some anime that star male characters (or supporting characters) who have fabulous transformations and all, like Kamigami no Asobi and Shugo Chara!, though it cannot compare to mahou shoujo since the magical boys aren't really the focus (for example, in Kamigami no Asobi they only transform near the end). I guess there's Saint Seiya/Knights of the Zodiac as well haha. But yeah, a full on magical boys is fresh for the picking, since there's not a whole lot of stuff out there. Don't worry though, I expect this to be a bigger thing in the future, especially if a lot of companies learn that there is a market for this (and the more mahou shounen anime out there, the better. Thank goodness for Binan Koukou Chikyuu Bouei-bu LOVE!).
OMG I almost forgot about the stripping rock star anime. Well, when the boys rock out, their clothes gets ripped off by the magical power of MUSIC!! (yes, they also fight evil people with music... as in they out-preform them in songs). I mean, they do look different, so I guess it counts as a transformation. =P
There is one manga that I've read is supposed to receive an anime adaptation. I'm not sure how to classify it, though. Mahou Shoujo Ore's about a girl who transforms into a magical boy (I believe there's another girl who does the same)... so it's gender bender, however, it seems like the costumes are what you'd expect a magical girl to wear. So the boys be wearing costumes like Sailor Moon (short skirts an all)!
There's a few more that come to my mind, but I think you get the point haha.
I don't like to ramble on and on