I don't want to mess up future quests by clearing places which are quest related so I was wondering if anyone knows any places, especially around the Whiterun area, which are not used for Quests at any point in the game?

With Radiant Story, alot of quests are in randomly picked locations.

I was thinking about making a list of all the quest-related dungeons (and therefore show that everything else is non-quest-related) because while you're worried about messing up future quests, I'm at the end of the game just wanting a place to fight stuff in.

I always end up at a quest-related dungeon that never respawns enemies or loot, and it's annoying. Bethesda should make a patch that fixes both our problems; a fix for doing quest-dungeons early and one for coming back to them later.

Not sure about that... There have to be places that are not linked to any quests.

Any location is up for grabs. Even the ones you've already completed. 30 game days after any location is cleared, Radiant Story will again consider that location usable for randomly generated quests.

"The game’s Radiant Quest System randomly generates new tasks based on your progress in the game. An innkeeper might ask you to hunt for bandits in a place you haven’t found yet, or an aspiring alchemist could request that you collect 10 undiscovered flowers for his work...."

"In addition to these minor tasks...you’ll be able to do extra work for each of the game’s factions, like th Dark Brotherhood and the Thieves Guild. Once you complete the scripted quest lines for each group, you can go to their respective hubs and pick up randomly generated missions to steal gems or assassinate shopkeepers across Skyrim‘s massive world."

http://goo.gl/mdntu