I've been playing this quite a lot lately and I find I keep gravitating to a mesh floor chimney design for my colony.
Current game I'm at cycle 143 and using a very simple narrow design.
Lowest floor is a pump in a small hole to collect vomit from the floor above, which contains my algae terrariums, and sent it to be filtered and added to my cistern, which is off to one side of the colony proper.
Immediately above the algae terrariums is the bio distillers in a sealed room to one side and the power apparatus to keep them running.
Above that is storage and a generator that powers the plumbing for the toilets and shower, and some compost heaps in a sealed room.
Above that is the microbe musher, ration box and associated power. To either side outside the mesh chimney design is the portal, the toilets/shower and two airlocked mines I use to collect extra water, slime, sand, dirt and algae.
Above the musher is the farms and above them the dining room.
Then it's the beds, and above them the unused medbay, which I plan to deconstruct eventually, and the gas pump that scrubs chlorine and hydrogen from the air and dumps them into a hydrogen generator, other gases are dumped at the bottom of the chimney to make their way back up.
The mines extend far more vertically than shown, with big tunnels dug up and down to access water and other resources. That tiling above the ladders in the top image was a funnel to direct water from the cave above into the pool on the left, which worked with only minor spillage.
Stress is 100% across the board, and in past colonies I've found it to be too difficult to keep it down in the long run, so this time I went 'fuck it! Embrace the vomit!' and just decided to make it part of the design. It now makes a small contribution to my cistern when it occurs in the main chimney stack, but elsewhere it is still a nuisance.
The air is highly contaminated as a lot of it came from the caves to the right hand side, which has a handful of Morbs running around polluting it. Since diseases are not really a huge problem I just decided to deal with it, so I have only a handful of deoderyzers now.
Scattered around are remnants of the original layout, which was a simple flat plan spread out on either side of the printer, and an experiment with cooling chlorine to a liquid to mop it up, which I abandoned when just destroying it with the hydrogen generator turned out to be easier and more efficient.