For the third generation games, it is known that FR, LG, Emerald and XD (and perhaps also the English version of Colosseum) have filters for two particular pokemon, Mew and Deoxys.
You must already know that in the 3rd generation, the capture data is stored for each pokemon, stating where it is caught, and at what level. The filters make sure that Deoxys and Mew are captured on Birth Island/Faraway Island and at level 30. If either of these criteria aren't fulfilled, chances are the pokemon is cheated, and the filter will deem them illegal, and thus forbids trading.
Other pokemons don't seem to have this problem, but I might be wrong.
Coronis~