I needed 13 anti-cubes when I caved in and hit the forums.
I am totally kicking myself about the telescope room, the little obelisks, the candle room, and the monocle room. I should have got those but once you start cheating it's hard to stop. Shame on me. I didn't get the clock room either but that was a bit of a pain so I am excusing myself there :P
I never got the number system so the bell tower, boiler room and 4 map room were totally lost on me. A number puzzle in that classroom where the numbers are explained would have been a nice subtle pointer.
However some were just so obtuse that they didn't make any sense at all. The throne rooms, metatron room and monolith are examples that require massive trial and error or leap of faith.
Still, it's a great game and I am pretty sure that the designers made the puzzles as tricky as they did so that people would have to discuss it and share ideas over the internet. It's truly brilliant.