1) Spirit Tracks. All the way, man. ST is the best, always, in my (perhaps twisted)book.
2) Twilight Princess, perhaps because I spent the longest on it first play through, perhaps because I'm spending the most time these days finishing off side-quests. (But, still, you could double the hours played and I'd still have done ST for longer. The first play-through took twice as long, crazy because yes, it is a shorter game. Five files... five files that I quit on. Now seven files completed.)
3) Phantom Hourglass. I don't love it as much as ST(dang I love that game), but it's a good one. But I've only finished it twice.
4)Ocarina of time, I rarely get time to play on a console these days. But at the end of the day, at midnight o' clock, I still have my DS
5) Link's Awakening. Because I adore that game, I just don't actually own it... yeah.
I've played just about all of them. But the most are:
1. Ocarina Of Time (not sure, I lost count a long time ago)
2. Majora's Mask (19 times)
3. A Link To The Past (17)
4. The Wind Waker (15)
5. Four Swords (GBA) (9 times)
Hmm... Compared to other people I hardly ever play o_o
1. Four swords adventures (4 times?)
2. Minish Cap (3 1/2 times)
3. Oracle of Seasons (2 times and 3/4)
4. Oracle of Ages (about the same as Seasons, I just don't play it as much)
5. Either Wind Waker or Majora's Mask... It's about even.
I've beaten WW twice and MM once, but I haven't beaten all the files I've made in MM.
Hmm... that's a tough one to remember, but I guess these four are the top 4 in no specific order.
As for the 5th I think that's going to go to Ocarina of Time if you count in the Master Quest.