I have to say that my favorite is Archipelago. Civilization III lacked a "true" archipelago map script, one with lots of small and tiny islands. CivIII's "water map" was more like "Continents Light". I tried a lot of things for this script. My work here is one of two key things on which I ended up basing all my other work, because it was with this script that I finally mastered using the Fractals. The core of the script ended up being as simple as could possibly be! The entire map is produced in one fractal layer.
The fractal process itself is a true gem. I don't want to go on and on about that, but it is the one critical piece of architecture inherited from CivIII. The CivIII maps (there were only three of them) turned the fractal loose, and so the variety of the land shapes was almost limitless. There turn out to be five "useful" settings for the "grain" of fractalization. This is a number that affects the internal mathematical calculations. That's all I can really say on that.
Never before seen screen from later in that first Deity game.
I had to kill over a THOUSAND mechanized infantry in post-modern combat to conquer the entire planet in that game! I got nuked a bunch of times, too, the AI trying to disconnect my oil.
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CivIII maps use the values 1, 2, and 3. 1 for Pangaea, 2 for continents, 3 for Archipelago. The Pangaea setting w[ould] not reliably produce a single landmass, though, so I ultimately had to go with other processes for CivIV's Pangaea. You -can- still get a CivIII-like Pangaea experience if you try the Tilted Axis script with Massive Continents setting. So CivIV continents still use grain value 2. Archipelago now uses 3, 4, and 5. I chose 4 to be the default. This is the "Archipelago" custom map selection. If you choose "Tiny Islands" you are playing with fractal setting 5. "Snaky Continents" is setting 3, just like the old CivIII Archipelago.
Getting the land forms right was actually the easiest part, since once I figured out that the fractals would do the heavy lifting, I learned which settings to choose and turned them loose. The really tough part of making the new Archipelago a great map was the map's balance in terms of resources and start locations. This is another one of those rare areas where I had to spend my political capital with Soren.
(Just as a quick aside, Soren's torture of me was the Civics system! We spent months and months AND MONTHS on that monster! Every time I thought I had a solution, Soren would send it back. "Cook it some more. It's not done yet." Arrgh!) Well, the start point balance was my torture of Soren. 
"It's not done cooking yet! Sorry!"
I sent it back to the chef over and over again. What we ended up with is not perfect, but it is significantly improved over where things stood in CivIII. We gave it a lot of attention and priority! This was especially crucial for multiplayer, where unbalanced starts could decide a game's outcome before it is even played. When we finally got the start plot process working gorgeously for 95% of cases, it was still failing miserably on the high grain maps (Archipelago, basically). So rather than further torture Soren, I wrote a different start plot finder for Archipelago, one that would not put two players together on the same Tiny Island, nor have them starting across the water from one another, two or three plots apart.
Never before seen screen from later in that first Deity game.
I had to kill over a THOUSAND mechanized infantry in post-modern combat to conquer the entire planet in that game! I got nuked a bunch of times, too, the AI trying to disconnect my oil.
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Archipelago will make sure to put distance between civs, while not sticking anybody in a craptastic location. There WILL BE usable lands in your area, though in some cases you may have to work to reach them. You may also want to "island hop" past some islands, when you can. Sometimes it is better to sail a little farther to a richer location, or to build your first galley -before- your first settler. A great city on the next island over may beat a junky little city on some barren corner of your starting island. The resources are also spread around nicely. That is another thing that got cooked over and over and over again until the flavor came out just right!
There are a few other little touches that I gave this script. I don't want to spill all the beans, though. I also know that Archipelago won't be everybody's cup of tea, but if you like this flavor, I worked to make it a richer experience!
The randomness on these maps is unparalleled! The only thing certain about them is that they will tend to scatter the islands all over the map. You won't see any large empty oceans. I was one of those guys who used to like to play the water maps in Warcraft 2. (Wow, that was almost a decade ago!) CivIV now has a true water map (more than one, actually!) and an AI capable of competing there. The AI is still stronger on land than it is at sea, so the water maps may be as much as a whole difficulty level "easier" than the same settings on land-heavy maps.
I love the exploration element of the new Archipelago map. You never know what kind of island is hiding out there in the fog! Will it be a large one? Small one? Will it have resources? Can I get from there to the next island beyond it? Or will I meet a strip of ocean that prevents further expansion in that direction?
BOB "SIRIAN" THOMAS | "Four Times the Charm" 