Yeah, Crystal had some songs exclusive to it that's not in GS at all (Eusine theme, Buena's Password, Battle Tower...).
In general all of the '3rd' games (Yellow, Crystal Emerald and Platinum) and B2W2 have reused tunes from the previous two, down to the same instrumentals. Note in the last two gens minor changes have occurred though in some reused tunes (e.g. some battle themes having minor changes here and there, although otherwise same tune).
IDK about some other spinoffs but Pokemon XD:Gale of Darkness also reused a lot of tunes as Colosseum, most remaining exactly the same (although some now used for different parts of the game).