As for the Companion Cube thing, that's interesting, but that strikes me as a bit of a Fan Wank [http://tvtropes.org/pmwiki/pmwiki.php/Main/FanWank]. Valve is on record saying that, from a gameplay perspective, the reasoning was what I said earlier; they designed a chamber where a cube had to be brought with you, but players had been trained to use them once and then leave them, so they need to convey that they should take it. It also served as an intro to the "Throwing things into the incinerator" mechanic, which is rather vital later. Now, that doesn't mean that it wasn't changed to represent a story idea as well, but it just seems to me like Valve never intended for the Companion Cube thing to get so important in the first place, and probably didn't attach such significance to it themselves.