Other applications are to do things. They should do the thing and get out of the way as fast as possible. Animation-induced delays are fundamentally contradictory with that; they waste the user's time instead of doing the thing.
Good and useful animations communicate something, they're not there just to be there or to make it "pretty", which is most designers use them. But they can actually communicate intent, action, immediacy and other important things, if they're used sparingly in the right situations, without actually getting in the way.
Probably the most basic animation most of us PC users see every day is the very basic animation of a text cursor blinking on/off in text fields, like the one I write it right now. It's super basic, but communicates that the computer is waiting for you, it's alive and you can enter things. If it was static, you get the impression something is stuck instead, or couldn't tell exactly where the cursor is at a glance. But it blinks, and that tells us stuff.
I do still like progress indicators when you might be waiting on a longer task (and when it actually indicates liveness, which too often it doesn't :( ).
Games I can sometimes appreciate the new user benefits and affecting the pace can sometimes have an artistic intent or relaxation effect that tools should not normally have. I have stopped playing games for excessive animations and will usually quickly (but not always immediately) disable anything that can be disabled. It is so common that I distinctly recall the free game Strange Adventures in Infinite Space intentially doing the opposite to great effect (it has been a bit but I think it was not only instant transitions but on mouse click instead of release).
