Brave New Wrold is really neat. The script may not be all that at times, but the new systems more than make up for it.
Yet Another Fire Red Hack, though it's main goal is not hard difficulty, is harder than the original and is very smartly done. It rounds out itself to the difficulty level of Platinum, and for something that can get steamrolley as Pokemon it does pan out pretty well.
Touhoumon Purple/EXTREME GRAPE is probably the most balanced of it's kind (meaning, a heavily hacked Pokemon game where Pokemon are replaced with Touhou puppets) when it comes to difficulty and battle polish, other Touhoumon games tend to be completely out of wack one way or another. A playthrough not knowing about the new battle systems will yield some additional difficulty, though a type matchup sheet is provided.
Chrono Trigger Platinum is pretty neat. It goes by things simply on the surface but pays off greatly by it. The other Platinum hacks by the same author are nice too.