So instead of, say, Skyrim Monster Mod just chucking werewolves into the world all over the place, they would be say, bandits for most of the time, and transform on a full moon? I've been mulling it over but am not a scripter and have no idea how to do about this.

There was an Oblivion mod which did this (I believe the most popular werewolf mod for Ob).

I haven't looked into this deeply, but you'd probably want to track the http://www.creationkit.com/GetCurrentGameTime_-_Utility, the game time, http://www.creationkit.com/GetSunPositionX_-_Game (who called it the Sun!?), and the http://www.creationkit.com/GetSkyMode_-_Weather. In reality, we have a Full Moon once every ~29 days in the middle of each month. The Moon is highest in the sky at midnight UTC. You'd probably want to abstract this information specifically for Skyrim time. Then, you'd need a script that synchronizes werewolf transformations based on the aforementioned variables to http://www.creationkit.com/WaitGameTime_-_Utility.

On the wiki, there's a section with example complete scripts. One of these tracks the stage of the moon.

It's not a full answer to your original question, but hopefully it'll put you on the right path...

http://www.creationkit.com/Complete_Example_Scripts#A_helper_script_with_functions_to_get_the_current_moonphase.2C_sync_between_the_two_moons_and_day_of_the_week

- Hypno

You would just have to setrace of the bandit to the werewolf race in a script when they are in combat or their health is low, etc. It would be cool after you are fighting them for a bit and when their health is below 50% give them a health buff and then trigger the transformation. I'd say forget the moon stuff you might never see it, plus skyrim werewolves can shift when they want anyway so why bother with a moon cycle? It's actually fairly involved to do the script, but you can copy a lot of code from the werewolf quest scripts.

That's a neat idea.

Tales of Lycanthropy does the full moons transformations in a way. It adds forced lunar transformations for the player, and if the player is not a werewolf, then there is a chance that the full or gibbous moons (Full moons being 75% chance, Gibbous being 10% I think) will trigger an event where a werewolf or group of werewolves will track down and attack the player. I think I've read that there are also hunters in the mod who may transform when the moons are full, but I haven't seen it happen myself yet. In Tales of Lycanthropy, the werewolf transformation triggers sometime between 8:00 PM and 8:05 PM, and transform back at around 5:00 AM.

From what I've read from the creator of the mod, getting NPCs to transform according to the moon phases is very script-heavy, meaning that you probably shouldn't go too overboard with stuff like this, and there is the problem that they will still use their assigned voice types when they are werewolves as well.
A link to the mod I mentioned: http://skyrim.nexusmods.com/mods/12687/