Favourites
Super Mario Galaxy - A lot of Mario games could be here like SM64, but I think Galaxy has some of the best level design out of any game in the series. The space setting is so well done and the whole vibe of the game is great fun.
Ratchet and Clank: Tools of Destruction - The first Ratchet and Clank game I played so it's what got me into the series. Arguably more of a shooter than a platformer, but the weapons are great fun to use making the combat great, and the controls are perfect making the platforming really good. Not a bad story either with good humour and likable characters.
Ape Escape 2 - Very lively game, the cheesiness is great fun and collecting monkeys is an interesting spin on the collectathon concept. All of the different gadgets add loads of gameplay variety and the levels are very fun.
Least favourites
Sonic Unleashed - Don't hate it, I just haven't played any 3D plaftormers I despise and this is just one of the more unremarkable ones. I didn't finish it as kid as it just didn't really hold my interest.
Banjo Kazooie - As I said, I enjoy the vast majority of 3D platformers I play so I can't think of any I actually dislike. I completely understand why people like this game, the humour and characters are great, it's very creative and has very interesting levels. However I didn't play it as a kid, so playing it for the first time a couple of years ago make it seem like it hasn't aged well. The controls aren't too great, and having to collect every music note in a level to improve your score made progression unnecessarily tedious. I also hated the hub world. It was cool, but it was just too big, and it was a pain losing health while travelling to a level, meaning to die more quickly and have to do the whole process again. I really wanted to like it as it has awesome qualites, but it could quite frustrating and I didn't finish it in the end.