Personally, i prefer any of the Boss Enemies over random annoyances found in the field, and this applies to any of the games. I just love the challenge, and a boss battle is where im at. always, in dungeons, when i encounter sub-bosses, it reminds me that i am halfwway there to the next good fight.
other enemies, slightly more common than bosses or sub-bosses, include DarkNuts and Iron Knuckle [those he who asked, they are different]. these enemies almost qualify as sub-bosses, as they are used as such on occasion, but you can also find them elsewhere. there is nothing quite like fighting three darknuts in
tMC, or a hoarde of them on the steps leading to Ganon in
tWW. and the Iron Knuckes in Ganon's Tower in
OoT are a nice change from the normal random sword fodder the evil forces throw at you.