Searing Spell is exactly the kind of thing I was looking for. A simple practical option that would allow someone to pose a serious threat to the character that doesn't outright kill them.
Sorry again for not clarifying before, but I'm approacing this more from a DM perspective than a player perspective. As a DM I don't believe in simply killing off player characters, unless they are victims of circumstance that they had all the resources to prevent. It's unfair to them because as the DM I've seen their character sheets and as such are totally prepared for them while they are totally unprepared for me. Moreover unless the story calls for it, it's also boring for me to build a party of somethings that perfectly counters everything the players can do.
The situation isn't really about an obnoxious player that needs to be put in his place. It's about an honest player that came up with a character idea that scares the hell out of me and wants to play it. He doesn't need to be killed, he needs to be challenged.
Sun Tzu's Art of War: Attack your enemies weaknesses and don't play to his strengths. That's about as realistic as combat gets.
Yeah but this isn't really war. Yet. It's a roleplaying game that tells a story. Unless the story calls for it then attacking the players weaknesses is not only boring but invalidates the characters. What's the point of strengths if you don't get to enjoy them?
A horizontal Gate to the Positive Energy plane opened above the character facing downward + Reverse Gravity? Instant death. Boring.
Encountering a crazy fire mage with the Searing Spell feat? Well he only does half damage (plus half again for cold subtype), so he's a threat that you can't simply march up to and facemelt. Now it's getting interesting.
Encountering a Master Spellthief with a caster level of 200-something? The entire party couldn't beat that. As far as I'm concerned those kinds of things aren't meant to be played. But if that's what it takes to pose a threat to this character then maybe this character isn't meant to be played either.
A vorpal sword? If it succeeds it's instant death. If it fails it does nothing. Boring. Plus vorpal is expensive and otherwise generally useless in a practically optimized environment. Few people are going to run around with it. The more frequently it pops up the more I begin to roll my eyes.
Graymantle and Remove Trait? Anyone who hunts trolls would have access to it, plus a little trollbane poison which ordinarily would be great. It won't kill you outright, and you still get to ignore rogues but you now suddenly have to worry about making saves and getting hit. Now you have to think again.
Trapping the Soul? MDJ? More instant death. More boring. As a player it's something I'd consider to kill an invincible NPC. As a DM I should be above that unless I don't want people to play in my games anymore.
Battlefield control? To slow him down I suppose. But beyond that it's a lot like asking the player to sit there and watch while everyone else plays the game. I don't know about the rest of you but as a player I'd be pretty pissed. I show up to play.
Domination? Turn one of the party's biggest assets into one of their biggest threats. Always a good option, especially if you let the player attack the party himself instead of telling him how to do it.
Of course eventually the party will become largely immune to it.
Then finally the biggest problem isn't the lack of options... it's the perpetual lack of options.
Realistically how many people are there that hunt trolls and take the Searing Spell feat? A few maybe, but why is it that we seem to run into them every single session, and they all want to kill us? Attempting to kill the players the same way over and over again eventually becomes just as boring as killing them outright without a save.
Thank you for reading the rant and for all the suggestions thus far.