When I first played through the game, I probably got stuck in the Forest Temple for the longest period of time. I still do from time to time, doing such things as forgetting about the twisted corridor or just forgetting where I'm meant to be going next. Although, the last time I played I got stuck in the Water Temple for the longest period of time as I couldn't find one of the first 3 keys that you need to collect, I really have no idea how I missed it. I went to the area that it is kept but just decided that once I'd arrived that I would just turn around again and try and advance with just 2 keys.
I think the hardest part about the Forest Temple was that I had to backtrack, as I was so young I thought that once I'd gone somewhere that I wouldn't need to visit there again, I guess I learnt a lesson by the time I got out of that place.