navigational elements flip color or something
Hover effects, if taken too far become what I call gratuitous motion and can be distracting.
But there are really 2 questions here, #1 is should you implement a feature on the desktop that won't be available on a touch UI and #2 is if you implement the desktop-only feature, what are the most effective parameters of that feature?
For question #1 I would say you can effectively use a desktop-only feature, but you shouldn't depend on it, that is if the feature were disabled the page would still be very functional and pleasing to use. The feature should be merely icing on the cake and not fundamental. E.g. mouse hover effects can provide useful feedback but if absent the site should still work well. Don't rely on them to the extent the site feels second rate if they are removed.
For question #2, what are the proper parameters to these desktop-only features, in other words how aggressive should these effects be, I'd say be very subtle here. There's a trend (not too popular thankfully) where UI elements are very active and flip around and expand and contract when mouse-overed. Gratuitous motion. These can be very distracting. It doesn't take much movement grab attention and interrupt one's train of thought. It takes the slightest change to effectively reinforce that something is clickable (the cursor change is enough really but a subtle change in the element visuals to reinforce the clickability can be pleasing). This extra mouse reactivity is rarely necessary, so only do it if it fits in well with the design as a whole.