The dungeon list I think is pretty much final (as much as anything COULD be "final" at this point, really), though the names might change.
I too expressed some concern about having an icy dungeon as the first. But I think it wouldn't be too bad, you can still have icy chasms and stuff which would actually be a simple, early-type of obstacle as the Roc's Feather is the first item in this game. I think something like Majora's Mask's Snowfall would work fine, but if that seems too dark and chasmy, perhaps something more like Twilight Princess's Snowpeak would work. That ends with a downhill "chasmy" area, and before that is a climb up a snowy mountain, but I was really thinking about the first part, which is a body of water with ice floes (is that what they're called?), which could also provide some water to jump over and hence the possibility of getting a Heart Piece or other areas once the Roc's Feather from inside is obtained. Anyway, we probably need more nighttime dungeons so darkness would work, here it's not like it's meant to be downright creepy, like the crypt stage later. But RT-55J should have input on this, especially regarding the dungeon entrance. Every dungeonmaker should have a say on what it looks like from the outside. But that won't stop me from making some suggestions in the meantime!
For the forest/flowery dungeon, I too was imagining large flowers on a cliffside that are open during the day. Many dungeons have a day/night requirement and for this one it seemed like an obvious choice. I was originally imagining large four-petaled flowers that open up (each petal would be another "standable space" in each of the cardinal directions to the center, also standable), but when it's nighttime, the entrance wouldn't be reachable since the flowers would be closed (Link wouldn't be able to even stand on folded up petals or bud or whatever, but mostly the petals aren't there to shorten the gaps enough to be jumpable). But now that I think about it, the flowers maybe ought to have eight petals, or at least be "fuller" so as to cover all eight squares adjacent to the center portion when open. It would make plotting jumps a lot easier.
I like your ideas for the Beach Cave, I have nothing to add. And we ought to have a few small "minor dungeons", like you mentioned. Not a priority at the moment, but if we have time it shouldn't be too hard to have a few. Minor dungeons are only a handful of rooms, right?
I've called dibs on the Horuglass Palace. I'd imagined it to be one of the few dungeons where it's actually playable in day or night, and the only one where there is a difference by doing so, but I think it should only be enterable in the day. Perhaps the player can still exit the dungeon via the main entrance to step outside to change the time to night, but they wouldn't be able to leave the screen of the entrance. Well, actually, it's more important that they're kept out at night rather than in, actually, so a one-way thing like a ledge might work. Anyway, the idea was that I'd make a five-floor dungeon which would actually look like it was actually an overall hourglass shape, with the floors reversed in the night. Lots of shifting sand and puzzles involving pits. For the exterior, I'm thinking it would be a giant hourglass, but it wouldn't be "clear" (ie. it's not meant to be read from the outside, stupid as that sounds). Maybe it could look like a big stone hourglass (maybe it'd look like the Pyramids in terms of large brick styling), or look like an hourglass carved in the face of a desert cliff wall. Either way, the entrance would be on the central part...the narrowest part of the hourglass, so maybe it'd be a big thing with stairs on a whole screen leading up to it, or the hourglass could be partially submersed in sand. The top part doesn't have to be fully built as there's no reason for it to be visible to the player, even if there's more of the map to the north (imagine Hyrule Castle in A Link To The Past, for instance). Hope that's not too complicated. Maybe it should be nearly half-buried in sand, that'll make it easier. (Or rather, half "under" the sand..."buried" makes it sound like it's physically stuck, which it can't be.) I do like the idea of hiding it in the desert, Lost Woods-style...
For some reason I hadn't put much thought into the outside and surroundings of the Clock Tower, depite the fact that that's probably the dungeon furthest along. I don't remember if I ever said that it needed to be day or night, but probably not, as it doesn't really matter, aside from the colour of the sky in my brief "outside" portion that's not really outside. You've seen that part, I assume. The Clock Tower is grey. Don't make me change it.
The Vampire's Crypt is definitely dark, definitely a nighttime thing. The name itself was under some contention (is that the word I'm looking for?) because some people didn't like the idea of vampires but because of the day/night theme I think it's pretty much a given that there should be a dark, shadowy, creepy dungeon that smells of death. Graveyards seem to be a staple of Zelda games, but perhaps a grand mausoleum/crypt entrance will be enough to make it unique. I seem to recall Ocarina Of Time's Shadow Temple to be little more than a hole in the wall, for instance.
Looks like we're on the same wavelength (ha ha) for the Temple Of Light. The Temple Of Light I imagined would also have angled mirrors rotatable (via Spinner gears) for the light puzzles, perhaps those could be outside, but more as a decorative thing since they probably don't have much real purpose with sunlight already everywhere outdoors.
Ask RT-55J what he meant when he thought up the Excavation Area. The "sneaking around" bit he wants to implement reminds me of the infiltration of the Gerudo prison camp thingy in Majora's Mask. So I imagine (and hope) that all that sneakiness will be entirely outside. As expected of such an area, there will be plenty of tiered holes, ladders, and piles of dirt, making for interesting sneaking terrain. And at this point most of the game's tools are available to Link, so tool-based solutions are possible too (perhaps there could be broken tracks that actually serve as Spinner tracks, for example).
I guess we still haven't come up with an idea for the major baddie. Any ideas? And any ideas for the name of the overworld?
It's cool that you're going to try to mix up the map a little bit. But I'm having trouble imagining the mountains anywhere but "north". The top of the map is where it's easy to put the sky and clouds as a background, giving the illusion of height. If the mountains are in the south, at best it'll just look hilly. And while sky isn't unusual in the middle of the map (like A Link To The Past's Dark World on top of the pyramid right in the center), I'd probably avoid it here. It'd stand out (a lot more than my suggestion to not have the hourglass necessarily complete) and while it might be something a real Zelda overworld designer might actually do, the awkwardness might clue someone in to the fact that all this is fake sooner than they ought to realise it. If you get my meaning.
The overworld must have features that involve the items. Most naturally, as a way to ensure a particular order of the dungeons, as discussed earlier. I already designed the Spinner gear switch and the Spinner tracks, which ought to be used for areas meant after the Clock Tower. We still need the dirt that the Mole Mitts would dig through, and the very similar rocky blocks that the Leever Drill would drill through. Other overworld elements are kind of a given. You know what they are. Caves where Rupees or Pieces Of Heart might be, or simply as a means of passage...some would have bombable entrances. A town-ish area. NPCs there but also in the wild, perhaps implying a sidequest. Trees with seeds. And you are already aware of the animal companion regions. Don't forget the Maku Tree! But I didn't really need to tell you all that.
Anyway, it looks like the overworld is in good hands!
Seems like you're asking the right questions and already have some ideas. I don't know how much I helped there...the dungeon entrances in particular will probably fall into place soon as the dungeons themselves get made.