I've toyed with the idea of modifying CFLs for 12v use, making my own ballasts etc but I've come to the conclusion that anything but a one-off is going to end up being a major construction project, and would probably eventually become a pain, especially when a failed bulb could mean getting the soldering iron out!
I guess you could incorporate CCFL inverters into the light fitting, and use the plug in tubes for those. It'd work for a few watts, and for small tubes you can match the tube to the inverter by changing the value of the high voltage capacitor on the output of the CCFL inverter. That would work for a 12v lighting system.
If I were you though, I'd probably use a combination of off the shelf CFLs (the candle sort, buy them in bulk from eBay) and incandescents, small 12w ones. I know I'll probably get flamed for saying that, but I don't think you can beat the light quality of filament lights for ambient/mood lighting, just don't install too many. When you need proper light turn on the CFLs. Just my opinion!
I found a neat way to run CFLs from a cheap inverter too - a cheap 'modified square wave' inverter will usually make CFLs buzz annoyingly and die early. The solution is to simply rectify and smooth the output at the inverter end, and use the high voltage DC for the lighting circuit. It works out much cheaper than buying 12v CFLs, and it's only slightly less efficient. Just thought it'd be worth mentioning!