The program is growing more complex with every release, so I figure it would be useful to have a manual of sorts around.  There is a color legend and a short instruction on recommended settings here, I hope it will be useful.

Go to the Color Legend
Go to the Recommended Settings Guide

Color legend
Atlas Color Legend

Junuxx's Recommended Settings Guide

Of course it all depends on what kind of map you like to see most, but there are some settings with which Atlas simply performs betters than with others. Those of you that don't like to fiddle with the controls for hours and the people that would like to know more about what each control does or what its boundaries are should be able to find some useful information here.

--- World Tab --- 
Let's start with Map Size. Optimal performance is guaranteed if you stick to the sizes featured by
Civ. The presets Duel to Huge are equal to the ones in Civ. Then again, I've had a lot of fun on maps
that were bigger than those, or maps that had different proportions.
Just experiment a bit, keeping this in mind:
  • Performance is significanty impaired on most pc's when you have more than 7000-10000 land plots.
  • Currently, Atlas needs at least 1750 plots to place jungles properly
  • I have not tested any maps with extreme proportions
    Some people say that any width/height proportion different than 1.6 impairs performance
  • I think Atlas performs best at the sizes Normal, Large, Huge and Giant
  • I'd avoid setting both width and height above 200 or under 20
Continents and Continent Size should be in proportion to map size, but I'd generally avoid setting size above 5 because of the blobbyness of the bigger continents. Except when you want an (nearly) all-land map. In that case a few size 8-10 continents should do the job. For nice continent maps, a lot of smaller continents produce the nicest continent shapes. For example, try a large map with 28 size 2 continents and 20 mixed islands. It will generally produce great maps with several larger land masses, more or less seperated by oceans.
With Islands and Islands type you can't do much wrong. I prefer mixed myself, but sometime a lot of lonely islands or a bunch of archipelagoes can give a funny effect.
Coastal Waters modifies the coastal water squares. 'Calm' turns some additional ocean into coast while 'wild' turns some water plots right next to land into ocean. This setting greatly influences the area you can reach with galleys, and thereby influence speed of expansion and contact with other civs. 'Wild' might slow your game down a lot on some maps!
Coastline modifies the continents' shapes, ranging from the nearly circular 'Blobby' and my favorite 'Irregular', which gives a fair amount of bays, peninsulas etc., to 'Chaotic', which gives frantically irregular continents and heaps of off-coast islands. Note that more irregular settings tend to produce smaller continents.
All I have to say about wrapping is that I'd avoid the setting 'Both' because it turns out Civ4 doesn't really know how to handle these maps.

--- Terrain Tab ---
Icecap size is the maximum width (in plots) of the ice caps at the northern and southern edge of the map. It produces peculiar towerlike formations with settings above 20, though. A nice setting for normal/large maps is 5.
Tundra size is the part of the hemisphere covered by tundra in percent. So 0 means no tundra, and 100 means tundra can appear from pole to equator. I advice settings between 0 and 40. If you are generating a tropical archipelago, be sure to set both icecap size and tundra size to zero! Deer only appear in tundra forests.
Forest and jungle size control the number of iterations of the vegetation placement algorithm. You don't really need jungles, but I recommend setting forest size between 2 and 4 for productivity, chopping, health and resources.
Mountain amount is the percentage of hills, times ten, turned into mountains. You don't really need mountains but you do need hills, so i recommend setting this between 0 and 6.
Hill/mountain amount is the percentage of the inland landmass turned into hills and mountains. You need hills for hammers, resources and windmills, so I recommend setting this to something between 20 and 60. Or, for a real alpine experience, make a all-land map with Mountain Amount = 6 and Hill/Mountain Amount = 75.
Desert size is the number of iterations of the desert generator. Best between 0 and 5, I think, and lower on very large maps.

--- Misc Tab ---
Starting locations is the number of starting locations the generator tries to place. It might end up with less. Those are then saved in the map file, but their number does not necessarily equal the number of players placed on the map. I'm trying to solve this problem though. When generating huge or larger maps, I recommend generating 18 starting locations. When you want to use Civ's starting location algorithm, set this setting to zero.
Minimum distance is the minimum number of plots between two starting locations. High settings may cause the algorithm to fail.
Resource abundance is the number of resources per 100 land squares. Can be set between 0 and 30, but if you do not want an unbalanced game, I advice you to stick between 5 and 20.
Land/Goodie Hut Ratio is the number of land squares per goodie hut. Higher values mean less goodie huts.
Amount of rivers modifies the number of rivers. Few is half of normal, and many is 1.5 times normal.