The main differences are the Motif you have a chance to get and any set item that would be unique to the zone you do the quests in. So, Craglorn would drop Martial Knowledge or Way of the Air, where Wrothgar drops Briarheart or one of the other two sets that drop in that zone. Thieves guild drops the Hew's Bane sets and Motifs, Gold Coast drops those sets and motifs.
The three that don't drop a set item are Mages, Fighters and Undaunted Delve Dailies. FG does drop a motif (Drauger) but not sure if the other two guilds do.
Bump, anyone else has any bit of useful info?