I have to admit that the rain thing is getting on my nerves ;-) My fort is in the swamp. It rains about 90% of the time. I am slowly getting roofs over everything, but the rain has really stressed out my dwarfs.
Not trying to pick on mikekchar specifically, but this serves a good example of something I've been noticing in this thread: a lot of people in this thread seem to have what I would describe as both an overly-optimistic view of their dwarves, and are not allowing for the fact that they are dwarves, not humans.
Listen to what you're saying for a moment. Imagine that you have been exiled to a flyspeck micro-town that is in a swamp where it rains 90% of the time, and for quite a while after you got there, there were few proper dry buildings... most things didn't even have roofs. There's no Internet, no TV, no radio, the entire town only owns a couple of books and you're not cleared to read them, and everyone is too overworked to have much chance of forming friendships. When you get a little time off, you drink it away in a ramshackle excuse for a tavern with the same people you hate at work every day, or you spend it in church, bleakly hoping, somehow, that prayer will make things better. One of the few breaks in the routine is when the overseers screw up, and you're sent out in the rain, yanking plants out of the mud so that you don't starve later.
Most people would be depressed! And that's *long* before you get assigned to hauling corpses, or desperately defending your terrible little town from horrific alien monsters. You've given a bunch of people grinding out bleak as fark jobs in miserable conditions a survival horror game to "brighten" their special days. And humans are far more suited and accustomed to such conditions than dwarves are.
Which brings around to the second issue: dwarves are not surface creatures. Rain being stressful above and beyond what it is for humans comes two ways: one is simply that it's a reminder that you are Outside. Outside is bad for so many reasons. The other is because, underground, if there is water leaking from the ceiling in quantity, *something has gone horribly wrong, and there's a good chance you're about to die*. From a dwarf's standpoint, standing around outside is super-stressful to start with (see cave adaptation), but rain cranks up the stress level immensely... the less stable dwarves are probably constantly stressed out because part of their cultural heritage in the back of their head is telling them 90% of their waking hours that they've been sent to breach an aquifer and are about to be sacrificed for the fortress's plumbing.
Consider that, as humans, many become uncomfortable when they are aware of massive weight just above them; people freak out in caves, mines, and less threatening claustrophobic settings all the time. Dwarves are the other way around; they are, as a species, basically agoraphobic. Ten million tons of mountain over their bedroom isn't alarming, it's *comforting*... because it's that many more squares of honest stone between you and the Horrors of Outside.
I'm not claiming the current system is perfect, or doesn't need tuning. But really, put yourself in your dwarf's shoes for a moment... consider what a dwarf's idea of a wonderful place is. Glittering caves, full of gems that sparkle; grand halls carved from the heart of the mountain, and engraved with the stories of their ancestors; "roaring fires, malt beer, ripe meat off the bone" to quote movie Gimli; wondrous crafts and ingenious mechanisms; and so on... all *very* far from a town in a swamp that rains 90% of the time and doesn't come with roofs.