Off the top of my head there's the quest for the Thieves Guild to steal Hrormir's Icestaff. If you haven't progressed far enough in the Mage's Guild questline to the point Irlav and Caranya are both dead, then one of them will almost always be present on the second floor of the tower. Which makes completing that quest a pain. The Archmage sleeps from 1am to 7am, but Irlav wakes up at midnight and stays in the tower until 4pm I think.
There's the Ahdarji's Heirloom and Sanguine Shrine conflicts.
I hear there is a conflict between the Thieves Guild "The Elven Maiden" where you steal a bust and "An Unexpected Voyage" where you deal with the Blackwater Brigands that causes the game to crash, but I never encountered it.
I think the Dark Brotherhood has a few conflicts with the Thieves Guild, where if you assassinate a particular target while a certain Thieves Guild quest is active you'll have to pay the blood price, but I forget which target it is and the quest it's associated with.