Okay so one of the antagonist of my RL game has recently encountered the party, and one firefight later managed to crawl away from a burning building without the players knowing. Now the problem is the guy is now effectively paralyzed from the neck down, and I ask how do I work that? I mean obviously he takes penalties, but how much and to which?

How could he crawl away if he was paralyzed from the neck down?

yeah I knew someone was going to ask that, he didn't literally "crawl" but he did manage to escape through assistance of unseen minions, the point is that he escaped and now he's paralyzed.

How about the old put your brain in a tank and mentally control your minions from it ploy?

BRAIN IN A JAR!!!!

Really, if the BBEG has minions use them, have him in a private hospital in some other country and be more of a behind the scenes guy.

Quite. Go for the "unseen puppet master" route.

And then, when your PCs find out who's behind it, and where he is...

Nothing says "Are we really the good guys?" like killing someone as they lay in a hospital bed.

Ok ( Using D&D like Stats )

Str and Dex are reduced to 1 or whatever is lowest - He cant move or perform any activitiy but blink breathe and piss in a tube.

Con is reduced in 1/2 affecting his HPs etc

He has no abilities/attacks or physical skills they are effectively 0.

He has no attacks unless psychic or someone throws/drops him and his wheelchair at the party.

His charisma could be intact though it could affect how folks see / interct with him so he could take a hit here as well.

His mind is his weapon now, and his charm/wit.

He could be very loved and respected by his allies who will rally to his side and seek to destroy the party. I see him waging a shadow war against the party, killing off/defaming/hurting friends, relatives, allies, engaging in smear tactics or trying to set them up for a crime, lose face, seem like villans. He would try to destory their credit <bank>. He would hire assassins to kill/maim them.

I had always meant for this guy to be a "behind the scenes" guy, hence the whole "burn the house down on top of the party" idea, but thanks for your suggestions, the hospital idea would give them moral conflict but I just like the idea of him in a wheelchair.

Psionics help also.

Another take - the guy is considered useless a joke and loses everything. His criminal/evil allies now turn on him and his assests like vultures upon a corpse. This forces the guy to seek out the party and seek safety from his own. Once a enemy now a client, who will parly his connections, knowledge etc to destory his former friends to save his ass.