There are lots of quest mods out there, but apparently few of them allow the player to choose how to handle a particular quest and give him choices that have actual consequences (for instance on the gameworld): as far as I know, there are:
- Juniper's Twin Lamps (some c&c with branching in the middle of the storyline)
- a number of quests in the LGNPC series allow for different paths and some of them have actual tangible consequences (the quests in Pax Redoran, particularly the ones when you become archmagister, are a good example)
- then there's obviously Rise of House Telvanni (which is probably the best example of what i'm looking for)
- Vivec's Fate allowed the player to choose different approaches in quests as well
- some quests in Tamriel Rebuilt

Are there other examples?

Hagge Island - 3 chapter long main quest with approx. 20 sub-quests. There is no English version though...

Some of the quests in The Sable Dragon have different paths or rewards, depending on choices you make.
Nothing too major, but there are quests and places when you can make a choice (even if it doesn't always seem like it at the time.)