First of all I would simply consider the replicator a story-element. If it is appropriate for your story if your characters can replicate a certain thing, let them. Of course in this case you need to keep track of these things, because what was possible in one episode should not become unavailabe in another withour reason ( the need to program the replicator with the necessary data, computer glitches, power failures, sabotage or computer locks are excellent reasons, e.g. ).
More generally speaking I would say anything that would not need specialized equipment nowadays ( comparable of course ), should be availabe via replicator. Certain high tech like computer parts, which contain very tiny connections or power supply lines, etc. should be impossible to create at least at a satisfactory quality. Crystal structures, organisms, etc. should also be invalid options out of the simple reason that the resources needed would be to high - a transporter system would be more suitable for such elements.
What I used as a rule of thumb, back when I was still playing Trek RPGs, was: If the player cannot explain how something works then the replicator cannot produce it, cause it is too complex.
We came in peace, for all mankind - Apollo 11