The only time I have ever choosen NOT to use a lens hood is when I'm in a hurry. If the extra few seconds it takes to put the hood on means that I'm gonig to miss the shot I want, I will go without. Otherwise the hood goes on.
The only other potential problem I can think of is the hood getting in the way when shooting macros. Sometimes the hood will cause shadows to fall on your subject, or block the flash.
As long as the hood fits properly, and doesn't cause vignetting, or shadows on your subject, I would leave it on.
"I thought that because fewer wolves meant more deer, that no wolves would mean hunters' paradise. But after seeing the green fire die, I sensed that neither the wolf nor the mountain agreed with such a view."
Aldo Leopold
Michael has read enough of my lens hood rants to be brainwashed by now...
Situations where a hood will cause a problem are very rare. The only two I can think of are using one on some lenses with a pop-up flash on an SLR camera - this may block the light from the flash in part of your shot. The other time would be in a macro shot at a very close working distance.
Lens hoods are mainly used to reduce flare, but another big advantage is physical protection of the front lens element too. The hood (as long as it's hard platic or metal) acts as a guard against bumps and keeps rain off. Plus they look cool. Dedicated hoods, which are the hoods made by the same manufacturer as the lens and specifically for that lens, give the most protection all the way around. The generic collapsible rubber hoods really don't do much of anything...