I don't recall how he lost his legs in his battle with Lucifer WAY back before he formed the X-Men... but he got his legs back after a brood had infected him and destroyed his body. His mind was transfered into a cloned body, which obviously didn't have broken leg.
Then later on he was in a battle with the Shadow King and during this battle (and I think his was mental) his legs were shattered again. So he was crippled once more.
Then during a battle with Cassandra Nova, she switched their minds and took over his body. During the following battle with Cassandra in Xavier's body (Xavier was in Cassandra's, which was comatosed) the mutant healer Xorn healed Xavier's body while Jean switched the minds back. This healed his broken legs so he could walk again.
A short time later we learned that Xorn was actually Magneto (note: in continuity it wasn't magneto but really Xorn, who made himself to look like Magneto... yeah, it's X-Men)... anyway... Magneto/Xorn reveals that he fixed Xavier's legs by bonding it with metal or something like that. He undid what he had done and Xavier becomes crippled again.
Then when Wanda did the whole House of M thing and said "No More Mutants" reality was fixed, along with Xavier's legs. This was never explained and probably won't be... but none the less, he can walk again.
And that's where we are at the moment.
Did I miss anything?