How about having to set up something in the past so you can use it in the future? Example: You really need a rotten apple. So you take your apple, put it into the past, go back into the present and there it is, rotting away...

I heard of someone doing that in a game with wine/vinegar, though I don't remember what game.

Sorry, i don't want to get too fond with this idea, incase another story wins the final voting, but as the puzzles will be a very important element, I think we should focus on them beforehand. Also, what perspective were you thinking? I'd like 3rd person, maybe over-the-shoulder. If the character's done right, then you'll get used to him and maybe start liking him.