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It looks like someone named Eishiya wound up finishing all the maps for this game.  Thank you!  It's great to see it completed!

It looks like the ones that I had made were taken down in favor of Eishiya's maps.  Oh well; I guess this way they will be consistent with the various small details.

That's going to be the case on any Linux/Unix based web hosting, which will be a fair amount of them.

Yes, (and I realize now I didn't imply this very well,) it's a minor thing, but it goes to show their quality when that's the biggest complaint I have.
Also I figured it would be worth mentioning for a site this size, in case that makes a difference.

I had them pegged as being on the "evil" side of the spectrum ever since they were making commercials that were more about busty women losing their shirts with a tagline of "see more at..." than anything that even suggested what their company does.

I use A2 hosting, and while I don't host anything near as big or popular as this site, I haven't had any problems with them.
The biggest complaint I ever had was that their internal file structures are cap sensitive.
I've also heard good things about Bluehost.

Switch servers.  I haven't been able to get my map fix on, and that's terrible.  I was worried the site was going down.

Hmm, maybe I was wrong then?
But that being said, that article already talks about unique elements to Link's Awakening.
Perhaps if it was "originally a remake of LttP" it was only for a very short time, like some of the devs wondered "hey could remake it on the Game Boy?" and so they tried, and when they saw how feasible it was they quickly decided to make something original.
The two games are different enough that I just can't imagine that it spent much time trying to be a remake before they turned it into something new.

If anyone wants to try their hand at mapping a 3D game, may I suggest this wonderful title?

If anyone here is unfamiliar with this game, I would compare it gameplay-wise to a Zelda game.  You have a single large world, but you can only explore certain parts.  As you go through the game you get new abilities and open new areas, and find new dungeons with new bosses to fight.  Overall it plays linearly with a progressing storyline.
Also, the game is charming and funny.  It has a lighthearted setting with food-related names and doesn't take itself too seriously.
Try to get a real copy because for some reason some emulators don't draw the speech bubbles right.

But after looking at the map, I understood why: while it superficially looks like a Starfleet ship with the saucer and the two nacelles, the layout is not based on any actual ship from the show and thus, generic enough that it didn't register as a Star Trek reference to me.

Well like I said, they were shaping the layout of the level into the Enterprise.
But if you wanted a stronger Star Trek reference, there is always that secret that leads to the bridge...

Perhaps it may not be that "hidden" because you do get an in-game map, but still, In Duke Nukem 3D, in the level "Warp Factor," the whole stage is laid out in the shape of the USS Enterprise.
Of course, you're on a ship, but it's not just that they shaped the ship like the Enterprise, but they filled out all the playable area to the whole shape.  There's no real proper reason to have access to places like the nacelles, except that they wanted to make the whole place shaped like the Enterprise.
And I never noticed it until I was poking around in the level editor.

That's not a swastika, that's a Manji. An old religious symbol that the nazis too, turned it the other way around and used it for evil.

Strictly speaking they didn't "use it for evil."  It's a symbol, and it symbolized an evil group of people, but the symbol itself isn't evil nor used for evil.
Also, "hooked cross" is the English name for the shape itself; swastika is only really supposed to apply specifically to the one that symbolized the Nazis.  "Manji" is the name of the symbol in Japanese, which is also what they called it in manuals and Nintendo Power, presumably to help mitigate any worry people might have had about there being a swastika in the game.

And speaking of, while we all may know that the dungeons were shaped like different things, what really blows my mind is that if you look at the dungeons in an editor, the whole underworld all fits together in one map the same size and the overworld.  That's REALLY impressive; because they didn't just "make shapes" but they made them in a way where they had to all fit together.  And with the maps people viewed, sure, people could admire the creativity in shaping the dungeons like things, but they never saw the limits they had to work with to achieve it, which would make it all the more impressive.

Likewise the Link's Awakening underworld maps (the caves and the dungeons) all fit together within large square shapes like the overworld does.  I haven't seen it all pieced together, but I do believe that they has multiple layers of maps though, so it wasn't as hard for them to make the creative shapes they used.  (But maybe I'm wrong; I haven't had the opportunity to view the raw map data.)

What were/are some of your favorite maps to explore?  Not just to looking at maps, which also can be fun, but I mean when playing the game itself, which games have been the most fun to explore?
I suppose I should also add "and why," though sometimes it's hard to really know "why."

Zelda games have always been my favorites.  Link to the Past ranks highly, and I remember pouring over that map for hours.  But I think I might have had more fun with exploring Link's Awakening.  The map int he library showed you only enough to tease you that certain things were out there, like a rafting area and a village of animals, but didn't actually show anything to you.  Plus I think the way everything was locked into a single screen really helped; you often could see the area beyond where you could access, so you knew stuff was there, but you couldn't actually access it yet.

I suspect that it was never intended to be a port of Link to the Past.
I bet early in development they just tried to copy over the map from it to help them test things.  Test the basic systems, test the artwork...

Trying to copy the map from LttP would be a good way to figure out what tiles you need, and how you need to adjust the art style to fit the restrictions of the console.  It gives a good concrete goal: can I copy this design into this tighter space?

Plus running around trying to play a map like that is great way to really push the game design into some realistic scenarios.  You can get a good feel for how different uses of space works and doesn't, how various enemy designs work and do not.  There is a great value in copying over a map like that; it's a lot easier to really run a game through its paces using a map that looks/plays like a complete one, rather than a bland empty field.

Porting over a game that is still selling on store shelves though?  I don't see an advantage to that.  I would sooner believe that early in development they were planning on this being a direct sequel to LttP than a direct port.

Here are two more simple ones... which do you prefer...
"2020 Super Baseball" or "Super Baseball 2020"?
"Super Noah's Ark 3D" or "Super 3D Noah's Ark"?

"Super Baseball 2020" and "Super Noah's Ark 3D."

When I look at the title's with "Disney's" in the title I would assume that the title "Disney" was just added on the cover as part of marketing, but if you look at most title screens they don't include the "Disney's" element.  Like how on the SNES there is a game called "Tuff E Nuff" not "Hey Punk! Are You Tuff E Nuff"  It's not a title, it's part of marketing.

A proper list might do the card-catalog technique and just have an entry like "Disney's Ducktales; see Ducktales"

And I'm not sure how relevant many of these are for older consoles, but I know many more recent ones have an internal title used by the console manufacturer; I know that consoles like the GBA, PS2, and Xbox all have specific numbers/codes assigned to each title, and they would likewise have specific titles assigned to them.  This data is also represented in game data.  I don't know if those apply to the NES or Genesis though...

Honestly, you can get a very comprehensive list from EmuParadise.
They took down all their roms but they still have everything listed.
The problem there is that the list is TOO comprehensive; they list duplicates that have any difference in the code, such as revisions and multiple regions. (The latter of which may be hard to distinguish between some titles that name the game differently in different regions.)

With the Genesis, it doesn't take very long to see that so-called "complete" games lists seem so different from each other.

Seriously; I mean where do you draw the line?
Do you include Sega CD and 32X titles?  They may have a different label as if they are different console, but strictly speaking they are still Genesis titles.
Should a collection like 6-Pak count?
And I get not wanting to count homebrew titles since most of them are tech demos, but then you have some that are legitimately full proper games, like Tangledeep and there was an RPG on the Sega CD some fans printed actual discs for.  But if you can't count them, then you couldn't count Gauntlet on the NES or Tengen's other unlicensed titles.

...One thing I will say, if you produce any list or distinct number, you really need to include with that the EXACT terms you are defining the list by.  Maybe something like "Title must have been sold on store shelves between year X and year Y without being taken down or recall for reasons other than poor sales."

Also, you might try asking your question on NesDev.com.  I know people there have shared sites that list a lot of various details, so someone there might have something to help you.

I would say they look better without the labels.  You don't want the background to be distracting, afterall.
The jungle would look nice.  Perhaps MG2's Building 1 Floor 1 might hit that right balance between memorable and looking good?  Plus it has a nice large section with no labels.

I think there are plenty of options for great maps to use for seasons; there's not really a need to recycle the same ones.  I think it's kind of a fun extra to stop by and see what map is being used, so I'd be in favor of seeing new seasonal images.
The only thing that comes to my mind though is that they might get kind "lost to time" if new ones are chosen every year, and I kind of would want to see some spot on the site that mentions what the previous background maps were.
I already can't remember what any of them were other than the Nemo one, and that I just remember because it took me so long before I found where it was from.

Do you also like the background images for the individual atlas pages?

Yes!  This is the greatest addition to the site behind doubling the random map sets!
And I find the choice for what map is being used for each console is just absolutely perfect.  I loved opening up various pages for the first time and thinking 'Of course it would be THAT map!"
Except for the lack of a Metal Gear background on the MSX page; that needs to be fixed.  Also the lack of a Rusty background on the PC-98 page, but that could probably be blamed on the lack of Rusty maps to begin with.  (But I guess that's a different subject.)

Did that come with a different piece in each box or something?

So the slight site redesign from a little while back has shown details from maps on the site background, and I love it.
On the main page they have been cycling through different maps, roughly with the seasons of the Northern hemisphere.  Last spring I recall it was a map from Little Nemo with a bunch of flowers.  Really nice stuff.

I've been able to recognize the maps, even if some took me a little bit of time.  But the one that's up there right now...  Alright, I give up, I can't place it.
It looks like something from a GBA game, but I'm not very certain.