On 2nd thought, there's one other thing to watch out for. If you use decorative beads or dots that can be easily knocked off, you'll have to pack them carefully, perhaps paper between the layers, in a hard container. Perhaps a good idea for chocoate dipped, too, just to be on the safe side.
Also I've never tried freezing lemon bars or other pudding textured bars, so I can't vouch for those.
On edit: David Lebovitz says about his lemon bars, "You can freeze the lemon bars as well for up to one month, letting them come to room temperature before serving", so I guess it's okay.
The only kind of cookies I can think of where freezing might be a problem would be something w/ a marshmallow middle. The texture might be altered when they thawed.
Every other kind--shortbread, marzipan, oatmeal, chocolate dipped, jam dotted or filled, and anything else under the sun comes out the same as it goes in. The only caveats are to let them cool first to avoid ice crystals, and to package in an airtight container to avoid absorbing any possible off-flavor.