Hmm,,,puzzle games in rpg's. I can't see why every rpg should include some really. First thing that comes to mind are the
adventure genre games such as the RR series, Tomb Raider, P Eve etc. FF7 was a classic in terms of testing the bounds
of logic....all good fun.
First of all, puzzles have to fit a role, ie to get from A to B....a good example are the Saga Frontiers...frustrating but hey...
even the earlier Suikodens are nail biting looking back.
Keep the puzzles simple, localised, realistic and relative.
As to examples....floor tile puzzles can be as complicated as you want to open doors, collecting artifacts for a person who
can help you continue on, finding those secret switches, text puzzles. All been done before, but its how you execute them.
Oh, and make the effort worthwhile...nothing worse than a 25 minute chase, just to claim a potion at the end of it