Good etiquette for map designers?
Wouldn't the worst thing be to have the user stranded without the cube? They may not realise they need the cube and try in vain to solve the puzzle. Wouldn't ending their game (and going back to an autosave) be the best option, or in some other way let them know they stuffed up.
For the storage cube, players should be able to get it back somehow. But Valve Portal test chambers established the standard that for the companion cube, you take it with you until the incinerator or end of level.
There's always the option of having a large pit instead of goo, and then having to walk back to a certain point where a staircase is.
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Letting them leave an area without required materials is very bad, IMO. Dont let the last door to the area open unless they have the cube in-hand. Maybe tell them that (via Glados) when they try to open it (via trigger, etc). . .or make them put the cube on a button next to the door, etc. All this is assuming you cant go back and get it, of course. . . if you can go back through the door again, then I am sure they will figure out they need the cube eventually. 
making the player stuck is extremely bad map design. The player should always be able to get a replacement cube. Imagine you just spend a lot of time on a level and now you are stuck. You may not notice it at first and spend a long time trying around different things, but nothing helps. This is not challenge, this is just pure frustration. If you want to create a "dead end" where the player could be stuck if making a wrong decission, Kill the player so that he knows that he did something wrong. But best is to avoid unneccessary dead ends anyway.