Truth about the Weighted Companion Cube
GLaDOS just said that it had to get incinerated to test if <Subject name here> could incinerate her/hes friends
The Cube is thrown down, technically you could think that in the game it is meant that when you put the cube down it, that isnt an incinerator but actually a SHOOT that drops it next to the end cake, DO NOT MENTION THE SECURITY CAMERA IDEA SINCE THAT ISNT SUPPOSED TO HAPPEN IN PORTAL.
GLaDOS just did anything to make you believe the cube was actually incinerated.
But why waste a cube when you can use it for the next test subject? 
Well, looking at the extense of the transport-tube network, I guess they have hundreds, no, thousands of cubes, both storage and companion cubes...
"Duct Tape is the answer."
Weighted Storage Cubes.
What they storage for?
Your specimen, where else do you expect it to go? There aren't any pipes connecting the toilet to the outside!
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no, the weighted storage cubes store luncheon meat and gnomes named sam
Teeny tiny portals inside the loo make removal of waste easy 
gepy wrote:"The companion toilet cannot speak, however it can take your crap."Journey - no idea on length = don't know the % done
The weighted storage cubes are there to make the weighted companion cube look better by comparison.