Specifically, doing the "Special Mission" leves for the Brotherhood of the Broken Blade and Azeyma's Shield will take you up a chain of leves, culminating in a boss fight against a strong NM. This final mission has a chance to drop Allagan Runestones, which may be given to Rowena in Ul'dah for parts of three different sets. The missions and rewards are as follows:

Brotherhood of the Broken Blade Special Mission - Operation: Bloody Scales
Byregot: Templar's Coif
Menphina: Buccaneer's Boots
Nophica: Harlequin's Cap
Thaliak: Buccaneer's Sash

Brotherhood of the Broken Blade Special Mission - Operation: Wolfsbane
Azeyma: Buccaneer's Tricorne
Halone: Templar's Tassets
Llymlaen: Templar's Sollerets
Nymeia: Harlequin's Tights

Azeyma's Shield Special Mission - Wanted: Tarbh Uisge
Althyk: Buccaneer's Shirt
Nald'thal: Harlequin's Acton
Oschon: Harlequin's Belt
Rhalgr: Templar's Haubergeon

Also, the Horn and Hand faction also has a special mission, called "Poaching the Poacher". It's aimed at lower levels, and doesn't have any unique rewards as far as I know. Also, all three factions have leves for levels 20, 30, and 40, which function a lot like standard battlecraft leves (The Horn and Hand leves are all non-combat except for the Special Missions), except they offer MUCH higher rewards. Also, if you use the "leve evaluation" function, and the majority of your previous leves were faction leves, you will be offered another one for free (One of the standard ones, not a special mission leve). On top of this, the reward will be boosted even further. Using leve evaluation on faction leves is how people can get over 100,000 gil from a single leve for a lodestone history achievement.

(For more info, check out GamerEscape's pages on Allagan Runestones and Faction Leves.