I'm thinking about going to an over under shotgun for all my waterfowling. Does anyone have any suggestions or advice? I usually only shoot 3 inch, but do they make a 3 1/2 inch in an over under?

Browning Citori Satin Hunter is a 3.5" gun.

I think Beretta makes one too.

I believe either Browning or Beretta discontinued 3 1/2 " over-unders. HK makes one too.

3.5" chambered over and under = major head ache. I will never have another one. It was a Citori and it was painful.

Yeah that's why they discontinued them. They are almost unbareable to shoot. The way over-unders are balanced, the bottom barrel is okay to shoot the heavy load because it is more in line with your shoulder, but the top barrel is above level of your shoulder, so it causes them to jump considerably and thus, quite painful. No way I would use 3 1/2's thru a double for ducks. Too much recoil too many times in one day.
But if you want it to use for turkey also, then I would understand.

Browning did drop the Satin Hunter but brought it back in 2006.
IMH0 3 1/2" shells in a 12 ga. borders on insanity anyway no matter in what configuration. If you feel the need for a 3 1/2 " 12 one would be better served with a 10ga.
They come with 28" barrels ad tip the scale at around 8 1/2 lbs. Now it you wanted to shoot 2 3/4 or 3 and use it for waterfowl and turkey it would be a good choice. The longer chamber would only add to softening the recoil with these loads a bit along with the back bored barrels. So many people think they have a 50 yd. gun but for 99% of the hunters this is only a fantasy.

Try the Ruger All Weather. They are a bit heavier and tough as nails.