Hard and fast answer:

If you have to stay in UI3 for 2 GCDs and there are 2 targets who will live long enough for Thunder do deal more damage than a Bliz 1, put a thunder on both.
If you have to stay in UI3 for 2 GCDs and there are 2 targets, one of which will live long enough for thunder to deal more damage than a bliz 1 (a boss) and a short lived target, cast a thunder and a bliz on the short lived target
If you have to stay in UI3 for 1 GCD and there is 1 target that will live long, thunder it
If you have to stay in UI3 for 1 GCD and there is 1 target that is short lived, bliz 1 it.

In otherwords don't cast thunder at the cost of spending extra gcds in UI3 and only if they will live long enough.