By far the toughest decision I've had to make (repeatedly) in Morrowind was whether to shut the game down and catch a few solid hours of sleep before work in the morning, or else finish what I was doing and enjoying, then go in to work on only 2-3 hours of shuteye or none at all. Some days, it goes one way, some the other.
Awesome. I'd imagine we've all been there a few times.
As for me, in addition to what was mentioned above, an ongoing tough decision I have is to wear a full set of Glass or a full set of Royal Guard armor. Weighing the obvious appearance, weight, and protection differences is so tough, I don't know what to do.
What I mean to say is that Morrowind is a game of decisions, one might not be harder than another, but it's so cool to see where your character ends up and realize that it was the result of many "tough" decisions along the way.