1. i enjoyed them all for different reasons. the only one i could put above the rest would be Wind Waker for it's cartoonish style. other than that, i loved them all. (outside of the 3D realm, Link's Awakening would be my favorite because it was the title that really got me into the series)
2. if you want to stick to the dark, realistic look, go with Twilight Princess. if you want some reference to Ocarina/Majora, go with Wind Waker.
3. i don't know much about the timelines, but i would say it fits after Ocarina/Majora, since they make reference to the Hero of Time.