Space Pilot 3000 was aired on TV the other night, and during the scene where Fry first falls off his chair, you can see Nibbler's shadow on the underside of the desk. This surprised me, as I never remembered seeing it on the original airing. I pulled out my DVD box set and found the scene, and sure enough I can see the shadow there too.

Its appearance suggests that the entire Brainspawn / Nibblonian story arc was conceived at the time of writing the pilot episode. However, there is a possibility that the shadow was added in at a later date, and that the broadcaster / DVD distributor is using that newer VT.
So, was that shadow visible in the original airing of the pilot, or was it added in at a later date?