The first time was when he tried to stop the alien Lucifer in tibet along time ago (first told in uncanny X-men #20). Lucifer got away by reliesing a huge trap on Prof, and his legs were crushed. Eventually his soul were transfered to a clonebody after it had been transformed into a broodqueen. And later Shadow King crushed them in the astral plane.
Thanks for telling the story about Cassandra Nova Xavier, I didnt know how it happened either, but now I do.
Xavier can walk now in the comics because Xorn (a new addition to the X-Men team, who's mutant power is basicly hyper-healing) healed his body in an attempt to mess with Cassandra's mind (suddenly being able to walk would be kinda distracting) and it was discovered after he was transferred back into his body, Xavier could walk because of Xorn. He still carries around a cane with him, since he's still having some trouble getting used to walking again.
And Cassandra actually switched bodies with Xavier, since hers was dying from pretty much every single disease known to man. When her body was close to death, Jean removed Xavier's mind and actually broke it apart and merged it with every mutant's mind on the planet. Cassandra attempted to take these merged pieces in order to boost her own power, but was defeated by Xavier and forced out, into the body of one of the Shi'ar Imperial Guards (Stuff, a shapeshifter who took on Cassandra's form, since her real body died) and is now trapped there.