Well, I have greatest hits versions of all the Spyro PS1 games with printed out "BL" covers. Then again, they're in DVD cases so yeah.
Anyways, in the case of Spyro 1, some of the music tracks for some worlds were altered to be more "original", Spyro 2 doesn't have any changes that I can recall, but Spyro 3 is definitely the biggest offender.
First, there's a cutscene that is supposed to play but for whatever reason doesn't in all BL and PSN copies. There are also some levels where their original musical track won't play, instead you'll hear a re-used song from another level. So, GH version is the definitive version of Spyro 3.
All that in addition to minor bug/glitch/loadtime fixes.
Also, not related to Spyro, but the GH PS2 version of Crash Bandicoot: The Wrath of Cortex has shorter load times than the BL version. So you have at least one PS2 example right there. Not to mention the whole Devil May Cry 3 situation. I believe the GH PS2 version of one of the Budokai games also has some added content, NQS.