By the way, possible spoiler alert for those that haven't played these three games.
My favorite Zelda games are WW, TP, and SS. My issue is deciding between these three because they all have something unique that I love and hate about them. WW has boss themes unique to each boss (mini-bosses aside) but the sailing is kind of boring (I am not as much against it as other people, though). TP was kind of easy, but Zant was too insane to not like. Also, WW and TP have my favorite Ganon in the series (WW has a Ganon with a good background, TP was the best looking one in my opinion, and both end in a one on one sword fight). SS was the most challenging of the three and caused me to feel relief after finishing off a boss (probably because the flawless motion controls caused me to be tired), but I have two main complaints: it was way too linear and there was one too many repeating boss fights (I'm looking at you Imprisoned). All three have great graphics and bosses (among them probably most of my top ten bosses of the entire series), and the stories were pretty awesome.