I entirely agree with the Imprisoned being one of the worst. Not only is the boss fight itself long and drawn out, it gets very tedious when you have to fight it again, with little done to switch up the boss fight (except for the 3rd one).
Bongo Bongo from OOT. Interesting Concept, even decent execution - but it's like five whacks and it's over. Stun the eye, whack whack whack. Poof done. After the shadow temple was so annoying to get through I expected more out of the boss and was disappointed.
Haha Moldorm in A Link to the Past was frustrating but so satisfying when you figured out how to beat him! In fact, most of the bosses were like that, which is what makes Zelda so rewarding. The hardest bosses for me were definitely the ones pre-Internet, when you had to keep using trial-and-error to beat them. Once you did though, it was the best feeling!