It's definately after infernal city.
Besides Bethesda claiming in a soon removed statement that the next Elder Scrolls games will be taking place after The Infernal City, we don't know that. Bethesda are the creators of the Elder Scrolls afterall, so they can change things around if they want and have Skyrim take place before The Infernal City.
All will become clear in about 2 weeks. :read:
As for the returning of old guilds or new guilds replacing them, I wouldn't mind either way. I just hope that people who aren't familiar the events that took place in the Infernal City don't raise up a storm that their favorite guild from Oblivion isn't in the game. The less "BETHEZDA R FAEL DEVZ 4 nO MAJUS GUELD" threads, the better.