I only lost the time needed to go back and get a stone, cuz I already had played the tech demo beforehand. Which really helps.
Basicaly you must first think, where or how is that going to move, then you simulate that movement with the mouse, keeping in mind to NOT grab it where the hinges are. The hatch is tricky on that too. But the hardest ones are levers, for me. All the rest is cake. Walking, like jens said, works too, but especialy for heavy crates and such. Sometimes just moving the mouse isn't enough. Think of it as pulling really hard with your tongue bitten.
I have read that this has been improved for Amnesia. But even still this was one of the greatest things I noticed when I first played it.