Outpost/Lookout towers in the Overworld:
The overworld is a nice area to build forests, swamps, deserts etc. and serves as a nice junction between dungeons, but it would be kind of nice just to see like... old towers blot the landscape. They may or may not have anything of importance, maybe just like 20-50 rupees and some enemies to fight. They're kind of like those sea platforms in Windwaker.
Other types of Overworld areas:
I've seen forests(almost too many, in my opinion), deserts(a lot here too), and plains in ZC... it would be kind of nice to see some honest to goodness swamps and jungles/coastal jungles/any unique kind of area.
Too often, I have seen towns be kind of... one use, where you visit it once, and then there's no real purpose to it anymore. In Link to Tortuga, Freedom has the town change just a little bit after each dungeon, making it kind of fun and interesting to visit it over and over again. The items in the shops changed, some buildings could be entered, some couldn't be and so on.
I honestly don't think this idea is overused, 2 quests have used it in ZC... I don't think that constitutes as overused. Either way, just have a water level that is raised and lowered by switches like the water temple in OoT.
Got the idea from Golden Sun: Lost Age when you reverse the direction the waterfall is flowing. You could design a dungeon based off that idea, have many series of waterfalls some flowing up, some flowing down, when certain switches are hit, the water flow could be reversed and certain areas could be accessed where others can't. This also could work for rivers and using the raft.
Well, I don't have much else to say, but I do know that scenery/colors won't make a dungeon, just because your crypt has skeletons and corpses doesn't make it any different from any other dungeon. Good dungeon design where the "element" of the dungeon or whatever is utilized in its design and puzzles, I don't have ideas for all types of elements, but that's where the community comes in. I'd like to hear your input
So post your ideas and input, we could get a solid idea thread here.