Conclave and Way of Life are the top ones to me, with Monks and Mystics and Reapers Due being right behind. They all apply to every playthrough. Conclave actually makes the politics matter inside the realm instead of it just being "make opinion high", and the favor system is very useful and fun. WoL and MM help give you something to do other than yet-another-war. Reapers Due vastly improves the health/sickness mechanics, adds hospitals and physicians and adds a system where your counties have a prosperity level that tends to increase with long periods of peace and gets damaged by war (as in losing sieges in the county, not you being at war elsewhere) and disease.
I'm not sure where to put Rome, most of it is very focused on its title, but retinues are really essential to me.
I'm also really fond of Old Gods/HF, because the pagan mechanics and new interactions are really fun. I like Charlemagne for the start date, but it's hardly essential. Horse Lords is good because it makes the nomads actually nomads instead of tribes, even for the AI. The silk road is also a nice addition (Jade Dragon also adds it).
Jade Dragon has some neat stuff, and adds some CBs that I really like having as an option, even if I rarely use them. Most weaken the absolute restriction vanilla has about "you can only go to war for a good reason" to "you can go to war for a bad reason if you really want to, but it will cost you". I think it's nice to have the option of going against the "civilized rules" for a price, much like how you can break a truce but it costs you. Sometimes it is worth it, sometimes it isn't.
The rest largely depend on what time period/governments/regions you want to play with.
The Republic is neat and well worth playing with, but it was added early in the game's history. They hard-coded a lot of the mechanics so they don't always interact with the more modular features from later DLCs the way they probably should. It is still quite playable, but a few combinations, like a reformed pagan republic when the religion only allows female rulers, are best avoided.
I don't have Sunset just because the idea seems to odd to me. (Disclaimer: I've gotten into two formal duels with a bear in my current play-through and that didn't bother me at all, so I'm pretty sure I'm not remotely consistent on this.)
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