Do the Stargate /Atlantis teams go through a decontamination process after every mission, is it ever shown? I know for example on Hand of God of the original Battlestar Galactica episode they show Apollo and Starbuck using a decontamination chamber and Boomer skipped using one to go to Apollo's bachelor party and contaminating the viper pilots so they all got very sick.
There's no specific procedure for decontamination for teams heading back through the Stargate, but it's worth noting that the entire base is a sealed facility. If there are any indications of alien presence (including an unknown viral infection) then a "foothold" situation is declared and the base is locked until it can be safely dealt with. On multiple occasions you see the teams being "checked out" by the medical staff after returning from routine missions so there's obviously a battery of prescribed medical tests that are carried out after off-world activity.
The same applies re: SG-1. Typically a team returning from an off-world mission seem to undergo debriefing and a trip to the doctor. On an occasion when a known deadly pathogen was suspected, the team also wore hazmat.
McKAY: Starts with respiratory difficulty, proceeds rapidly to fatal organ shutdown.
(Walking over to the others, he sees their expressions as they look at him still cleaning his hands.)
McKAY: Oh, it's disinfectant.
SHEPPARD: We just came back from the bio-screen, Rodney. We were wearing Hazmat the whole time, too.
McKAY: Yes, well, it's better safe than sorry.
Medical scans (before and after gate travel) are apparently pretty common.
KELLER: Well, maybe, but not necessarily. It was too small to show up on a scan at the time; but in the Pegasus galaxy the condition is fairly common among the very old.