If I recall right, a Pokédex revealed a ghost Pokemon that was creating an illusion. Were they ever used in a novel manner, like to communicate or identify tracks?
I believe the Episode you are looking for is this one, whereby the Pokédex picks up an impersonating Gastly.
Yes, the Pokédex has been used for other situations other than identifying a Pokémon
Taken from Bulbapedia:
They may give background information on the habitat or activities of a Pokémon in the wild or other information on the Pokémon's history or anatomy. Pokédex entries also include height, weight, cry, footprint (prior to Generation VI), location, other forms, and a picture of the Pokémon.
This is seen in Episode 110, The Stun Spore Detour, where Misty uses Ash's Pokédex to search for a natural antidote for paralysis.
In Pokémon Adventures, Blue uses his Pokédex to 'transfer' his Porygon into Yellow's Pokédex.
The Mankey troupe promptly starts to lose focus with their leader's distraction. Coordinating with Yellow, Blue sends his Porygon through his Pokédex to Yellow's, which emerges through Yellow's Pokédex and faints Primeape with a Tri Attack.
Bulbapedia - Book 5, Chapter 55 Pokémon Adventures - The Primeape Directive
You could say that the Pokédex was used as a method of communication in that scenario.