I suppose you could cool the gas down into a solid?
Yeah, that'd be cool. Some sort of freezing gun that sucks in air, super-cools it (it's a comic book
), and shoots it out as a liquid at a decent range. The liquid air would of course quickly boil so there would be a steamy effect around the spray, and it's range would be limited by this (eventually it would all boil and slow down as it dissipated into the warm surrounding air). Anyway, I imagine your villain would panic when the gaseous form condensed into a (floating?) liquid form, trying to squirm away at this point; after reaching the supercooled solid form, he would be immobile and contained, but only as long as he remained cooled (he could also be partially solidified, and escape as a liquid, losing perhaps a limb or something that he left behind as a solid poison).
Or perhaps some chemical reaction that neutralizes the toxicity of the gas? That is, mixing the poisonous gas with some chemical which reacts with it, forming a non-toxic product.
Or suck him into a vacuum chamber! Yeah. A vacuum gun. Has an extendable nozzle, which allows distanced vacuuming into a chamber on the back using a motor on top of the chamber. The room might lose a lot of it's oxygen due to the vacuum gun taking the air out of the room and putting it into the chamber, which means a) the vacuum chamber on the guy's back would get heavy, and b) the guy with the vacuum gun would probably have to also use some sort of oxygen mask or something to allow him to breathe.
Or mix some radioactive elements into the poisonous gas so that you could... err... track him. Then... maybe shoot him when he returns to human form?
Or something.
Also, no matter what, your hero could remain invincible by simply using a gas mask. You could perhaps factor in particle size in air filters (I've been working with filter data lately; here's a chart with particle size information:
http://www.sterlitech.com/pdf/filtrationspectrum.pdf)... like where someone uses a filter where the minimum size of a particle the filter can block out is not small enough, and the villain gets in with an evil laugh.
Or something.