I needed some atmospheric damage rules for my last space opera game, and so found something in GURPS Space that I adapted to my game. These rules are fairly loose and need a lot of GM disgression.
A slightly toxic atmosphere requires a CON roll every hour or so. Damage should be in the order of 1 to 2 points, either automatically, or after failing against a toxicity level of 4 to 6 on the resistance table.
Toxic atmospheres need a CON roll every Full Turn, for the milder atmosphere, to every Combat Round for the deadlier types. Damage is 1d8 either automatically or after failing against toxicity level 16 on the resistance table.
Deadly toxic atmospheres would need a CON roll every Combat Round, if the GM is feeling generous, or a luck roll. Damage would be 1d10 upwards plus possible heat (page 223-4 in the BGB) or acid (page 211) damage as well. The toxicicity level on the resistance table should be at least 25, possibly more.