[NAME] - why three names?
Singluar/plural/descriptive. The most obvious example of the latter being used is during description of sites - when you see, say, "the goblin dark fortress of goxasnodub" the third name in the creature entry is being used for "goblin". If I were to change the goblin entry's third name to "grotesque", it would show up as "the grotesque dark fortress of goxasnodub", etc. I'm not sure what else it's used for in the current version.
[TILE:151][COLOR:2:0:0] - I get Color, but is tile the image icon it uses?
Yes, either a character in inverted commas (eg 'c') or a specific tile from the tileset currently in use (data\art).
[VERMIN_FISH][FISHITEM] - I get that these are the attributes of the creature, but are there any other tags I should know of? Can I find a list of them?
List of modding-related pages on the DF wiki. Anything else you need you'll probably be able to find there.
[POPULATION_NUMBER:25:50] - what does this mean, why two numbers? Is this the local area population max?
You're close. The number of generated turtles per pass in worldgen, and the maximum number that can spawn on your map (in fortress mode) in a given year, is always between those two values.
[AMPHIBIOUS][SMALL_REMAINS][NO_WINTER] - Again, attributes but are there other tags and is there a list of them?
Answered above
[SPEED:2900] - I guess this is movement speed?
Specifically land/air movement speed; swim speed uses a seperate tag. Standard (unspecified) speed is 900; lower values are faster (this is different to the displayed speed value in adventurer mode). For a poor comparison, elves are 700.
[PETVALUE:10][NATURAL][PET] - I get the tags, but what is the value range and are there other tags?
Value range? The value's whatever it is. It can be set to anything that isn't ridiculous and causes an overflow. It can even be set to negative values if you need to do that, for whatever reason.
[NOT_BUTCHERABLE][HASSHELL] - I get these tags, they involve cooking/eating but why can't you butcher a turtle?
It's a vermin. Vermin aren't hunted or killed as such; therefore they have no need for butchering. The equivalent values with fish vermin (see the FISHITEM tag above) is that they need to be cleaned. I don't know about large water creatures, but they're bugged in the current version anyway so you're unlikely to see them unless they exist directly on the map when you embark.
[PREFSTRING:beauty] - ... what?
This controls how the creature is described in an inidvidual's preferences ("Urist likes turtles for their beauty"). Add as many lines as you want and they'll get picked randomly when someone likes the creature. There's a more general "description" tag in the next version.
[DIURNAL] - ... what?
Diurnal as opposed to nocturnal; the creature is active in daylight hours. Not very important right now, but better to put it there anyway.
[BIOME:ANY_POOL] - Biome: where it lives. Again, is there a listing of these tags?
Again, the wiki.
[STANDARD_FLESH] - as opposed to carapace, undead, or other flesh, I get it.
Nobody really knows what STANDARD_FLESH does - it might determine some default values for ignite points, boiling points, freezing points, etc, which are fairly realistic. Removing it seems to make a creature reasonably immune to freezing and the like unless you specify another value (with the COLDDAM_POINT tags and such). Don't take my word for it though.
[SWIMS_INNATE][SWIM_SPEED:2500] - would love an explanation
SWIMS_INNATE as opposed to SWIMS_LEARNED; the creature has an innate ability to swim. SWIMS_LEARNED means the creature needs skill in the "swimming" skill to swim; this naturally requires either CAN_LEARN or SLOW_LEARNER. I mentioned the mechanics of speed above.
[POPULATION_NUMBER:250:500] - again, what is this? Total pop possible?
Why is there a duplicate of this? Odd. This value is more appropriate for vermin creatures; the earlier one would've been better for herds and such. Note that you won't be seeing them all in one large group; as I said, this is the number of creatures generated per pass. There's a seperate tag to help control "pack" numbers - CLUSTER_NUMBER.
[MUNDANE] ... what?
Not really used for much at the moment. You'd probably do well to add it to anything that isn't fantastical.
Edit: Ninja'd - and I was so close as well.