In terms of looking for a good mod, I'd advise:
1) The Last Days. Though Tolkien isn't to my taste, it has a war system whereby your the outcome of your battles influence the wider war, and the new objects, skins and meshes are very good.
2) Storymod. Jazzes up the vanilla game quite well, by including loads of new weapons, items, and the Arena mod which makes fighting in the arena an interesting and profitable activity. Oh, and it has a new faction with new cities, and a plot to follow.
3) Onin no Ran. Far from finished, but it has a nice large map and allows you to recreate Shogun Total War type battles, which is good fun and a change from the Medieval style stuff.
Craftmod is quite impressive technically but needs to be integrated into another mod like Storymod, I reckon; 1066 has some questionable design choices as mentioned above (you can replace the sounds though); A Shield Lying On The Water is promising but under heavy development. The Lombard Leagues looks quite interesting, whenever it's released. Dukes & Mercenaries needs its own map and factions but has a lot of new Renaissance era weapons and items. Pirates is technically very impressive but to be honest, naval battles aren't really M&B's strong point IMO.
I'm sure I've forgotten a couple, but most other mods don't really do it for me - too obviously unfinished or don't mesh well with the basic game system (as well as Pirates, mods like Star Wars come to mind.)
This thread does alert me to a fact though, that mods aren't very high in visibility amongst many M&B players. Every M&B player should know a) there are modules existing which expand the game, b) where to get them, and c) how to install them. When M&B is more finished, I'd advise Armagan or whoever to have a section on the taleworlds.com website specifically for modules.
Oh, and before I forget, Battle Size Changer is a must!