Like Walter, I've found they do more harm than good...
'Twas a Microsoft "IntelliMouse" that finally drove me to use a trackball. After about a year using the thing, my right wrist hurt so much I could barely stand to use it at all. It took me about a month to get accurate enough with a trackball that I could comfortably resume image editing and gaming, but by that time the pain had also subsided, and hasn't returned.
For me, the biggest problem with the "ergonomic" mice is their tendency to fit my palm. And I know that probably sounds like a good thing, but, heh... It meant I was able to rest the heel of my palm on the back of the mouse, effectively palm-gripping it even when at rest. Which was wonderful for my accuracy when pin-point accuracy was required - my palm stabilized the mouse while I used my fingers for precise movement - but was a constant and unnecessary strain when, say, scrolling through a text file or web page.
I may try a mouse again when one of my trackballs finally wears out, but if I do I'll be careful to choose one too small / short to contact my heel or elevate my wrist.
FWIW, I also hate ergonomic keyboards. When I experience pain from typing, it's from hitting the keys too hard - the best solution I've found for this so far is a keyboard with a decent amount of travel on the keys, and good tactile feedback - my 20+ year-old Model-M is the gold standard for typing comfort in my book. All a split/bent/warped/twisted layout does is cause me to make more errors when typing, magnifying the damage caused by each each tap.