I think its safe to say that we'll get
1. Blades (they may not be called blades and they've been part of main storyline before...)
2. Fighters' guild
3. Mages' guild
4. Thieves guild
Those are bread and butter of Elder Scrolls games.
I'd love to see the returning of religious guilds. Knights of the nine was a fantastic addition to the lore, but it could be expanded.. One could serve not only as a knight but as a full time monk, scholar, healer or priest. And since we are in skyrim, maybe something centered around Nordic religion. An order of monks worshipping the ancient dragon gods or something. Just be creative.
Also Oblivion lacked the political factions which was best part of morrowind faction system. I feel that we have a great chance of experiencing something similar this time around, after there is a civil war going on. A strugle for power. Clans without leader, kin against kin. A great setting for political factions similar to great houses.
A proper assasin/criminal guild would be a nice addition too for the evil characters.
Evil mages need more love too. The mages' guild needs an opposing faction, not necromancers though, they are boring. Something linked to Dragons or Daedra worship. It svcked that if you played a shady magic user, you would still have to join the mages' guild to get proper training and so forth
Last but not least, the vampire clans should return. Make the journey to darkside worthwhile