My favorite? Well I guess it would have to be the Pokémon Ruby Destiny series with it's amazing storylines in the trilogy, only RR and LoG had some music from other games in it. But it's understandable that RoL had the default Ruby/Sapphire/Emerald music, 'cause it was a very early ROM hack that was around before any of us PC members had discovered about music hacking and all that. But once we did, that's when ROM hacks in the generation 3 part became more interesting.
But apart from the Ruby Destiny series, which I'd recommend, you really should try these ROM hacks:
→ Pokémon Light Platinum
It has a great storyline, has a nice tileset freshly prepared, only one downside to it though... it has the default Ruby/Sapphire/Emerald music. But I'd still recommend it.
→ Pokémon Flora Sky
It too... has a great overall storyline to it, as well as freshly prepared tilesets and default Ruby/Sapphire/Emerald music, but I recommend it too... since it was inspired after Shaymin's Sky Forme from Pokémon Platinum.
→ Pokémon Liquid Crystal
It is a remake of Pokémon... well you guessed it, Pokémon Crystal Version, but with some twists to it and some new features! It has remixed music from Pokémon Gold/Silver/Crystal, and it has new tiles added into the ROM hack and it's a ROM hack of Pokémon FireRed Version.
→ Pokémon Snakewood
Probably one of the newer ROM hacks here on PC, it has a magnificent storyline to what happens in the game, it takes place in the future Hoenn region, it is a ROM hack of Pokémon Ruby Version. Something I would also recommend you should try.
→ Pokémon DarkDiamond
This is pretty much the only ROM hack of the Nintendo DS ROMs that has (or is going to have) map edits, this is a hack of Pokémon Diamond. You would be amazed by the changes this ROM hack really has, I would really recommend it. It's one of the first of the 4th generation ROM hacks that have edited map layouts in it.