As usual, Castlevania takes a hit, but really wasn't that bad...it just couldn't live up to Nintendo's 3D entries. The whole transition to 3D could be seen as problematic, Metroid and GTA are probably the only series that actually improved in sales (maybe Zelda)? Super Mario 64 was a good game, but jdging by sales, @The_Liquid_Laser is not the only one who disliked it.
I personally found the GameCube gen was lacking for Nintendo. Super Mario Sunshine, Wind Waker, Paper Mario: TTYD, all left me cold compared to their N64 counterparts, and I was really feeling the loss of Rare. Not saying any single one was terrible (in fact for a long time Wind Waker was my favourite even though I recognized it was very flawed) but the ongoing let downs added up to drain my enthusiasm.