I had found X Men 200 (and like you was disbelieving at the epic slashiness of That Scene) but I donlt actually remeber Maggie running the Mutants (which is funny as I had quite an intense pash for Ilyana) - so what issue nos was that??

Magneto officially takes over as Headmaster in New Mutants #35, and most of his scenes are from that series. They're well worth checking out.

And ah, Madeleine. She was a clone, and then she was manipulated by Sinister into becoming the Goblin Queen, and then she was defeated...and I guess died for a while? I'm not sure, I missed those issues of X-Factor. But she did appear in X-Men as a villain sometime in the last couple of years, so she's still kicking somewhere. And the Nathan/Cable thing...I'm not even sure *I* get it. :P