My two favourite generations were the 4th and 5th. However, out of the two you specified, I feel this gen is ahead.
This gen, the DS, PSP and Wii have all surpassed my expectations and I have kept the quality of this generation very high. However, I feel let down by my PS3, don't get me wrong I've sunk well in excess of 100 hours into LBP and I don't regret my purchase at all, but the platform hasn't thrilled my in the same way that the DS, PSP and Wii have.
Anyway, my favourite 6th gen games:
Skies of Arcadia/Legends
Tales of Symphonia
Tales of the Abyss (however only played the 2011 3DS port)
Snake Eater
Metroid Fusion
Metroid Prime
Metroid Prime 2
SSBMelee
Paper Mario TTYD
Zelda Wind Waker
Zelda Twilight Princess
Zelda Minish Cap
Fire Emblem
And to contrast, my favourite 7th gen games:
Xenoblade Chronicles
SSBBrawl
Super Mario Galaxy
Super Mario Galaxy 2
The World Ends With You
Little Big Planet
Advance Wars: Dark Conflict
Pokemon Black/White
NSMBWii
Demon Souls
Zelda: Skyward Sword
Metroid Prime 3
Donkey Kong Country Returns
Mario Kart DS
