I've heard from a few places that Spirit Tracks has some of the toughest puzzles they've seen in a zelda game, so i'm wondering what you think is the toughest?
personally i remember getting stumped a lot in Oracle of Ages. Maybe it was because i was younger then, but that game certainly had more to do with puzzles than combat.

I've not made it past the title screen of Twilight Princess yet.

I'm not sure but the water temple in OOT was a pain in the ass.

I thought Master Quest had some crazy parts in it.

The original Zelda on NES.

 Zelda II: The Adventure of Link

The original Zelda, for sure.

" The original Zelda on NES. "

There is a ROM hack of a Link to the Past called Parallel Worlds that is supposed to be the toughest in the series.  If you want a legitimate choice, I would have to say the original.  

Some of those later tunnels in Zelda 2 are tougher than the stuff in Zelda 1 IMO.  Both are tougher than more recent Zelda games.

OoT because of that stupid water temple

Zelda II. I can't stand playing that game for more than twenty minutes because of its absurd difficulty.

Hmm, for me the toughest would be either Master Quest or Zelda II however for bad reasons. A lot of puzzles in master quest were really stupid. Like you just have to know to hit cows with bombs without any indication. Zelda 2 also had cryptic crap too, although I suppose it is slightly more excusable since games of the time had a tendency to pull that crap.

Oracle of ages I felt offered the most genuine challenge when it came to puzzles. Some of the dungeons really tested you and the solutions were never obscure or asinine.