Well I'll say Colosseum/XD were good. As for spin-offs I'm not sure about the Pokemon TCG GBC games or Pokemon Ranger because I haven't played Ranger in a while and I don't have the TCG game. Red/Blue gets a mention because that was my first handheld Pokemon game and X/Y are okay, but they remind me of B/W because there's not much to do if you only pay attention to the key points of the games and not all the items. I liked X/Y because it felt easy to explore and I found most of the TMs without any help. Colosseum had the best content and new concept. Red/Blue (like the Gym Leader and Champion themes) had the best music of all the games next to the DS (D/P Battle Tower, Vs. Origin Giratina, Vs. Suicune, Vs. Ho-Oh, N's Castle, N's Farewell you name it) and GCN (Miror B. themes, Semifinal and Battle SIM, Final Battles against Cipher Head, Lugia) ones. Pokemon Ranger was the best spin-off (next to Pokemon Snap which would be neat for the 3DS/Wii U as well as Ranger). Not sure about Mystery Dungeon, Trozei, Typing, Dash, or Pokepark, Hey You Pikachu!, but they don't seem like the best. As for spin-off music I'm not sure if I'd prefer the TCG or Ranger because I haven't heard Ranger in a long time but I might remember the capture Entei music. For story, the GCN games were neat and B/W were just as good but less personality as the GCN games (and Red/Blue got the basic story down perfectly fine). Stadium 1, 2, and Revolution get mentions because you could battle Pokemon with other people in 3D and PBR had online matches but if Colosseum/XD had online it would have made it twice as good as any of them.
The winner of the "My Favorite Game Ever Award" goes to Colosseum, the innovative deck of cards.
For Spin-offs... You cannot compare them. They are too different but I'd say Ranger.