So i have come across several collection quest so far, bear pelts, nirnroot, crimson nirnroot and a few others.

Is there a list of the different collection quests anywhere so i know what to keep while levelling?

http://www.uesp.net/wiki/Skyrim:Miscellaneous_Quests

and you can't get rid of quest items until you have the quest that's associated with it. so, if you pick up a quest related item you can't sell, drop or store it until you have the appropriate quest.

as for normal type ingredients and such for quests the only ones that are hard to replace would be crimson nirnroot. beyond that, you can find most other things with little or no problems.