Per FITorion's earlier answer, the 'Mystery Object' referred to in the Crew Commentary for "The Gathering" is known as the Oscillation Overthruster
Voice of God (JMS himself) stated that John Navarro knows what the object is;
Now it's driving me crazy -- did John ever tell you what the mystery
object was that has supposedly appeared in every sci-fi movie/tv
project? And, more importantly, is it true?
Yeah, it's true, and no, he wouldn't tell me.
There was a group of folks in the art department who were referred to jointly
as the Woodland Creatures...Dark[Hoffman], Bear [Burge], and Dragon (two of which are real
names, the third is a nickname, I'll let you do the investigation on that one).
There could not have been a more apt description of these guys...
And an archived interview with John Navarro on JMSNews confirms that the object in question is the "over-thruster" originally used in Buckaroo Banzai;
"Well, this thing has been driving me crazy for several days, and I
finally found a bit of time to comb through some old interview notes,
and I'm 99% convinced that the object in question is the over-thruster
from Buckaroo Banzai. During production on B5, I spent a fair amount
of time with the props guys Bear Burge and Dark Hoffman, and they were
nice enough to give me a tour of the prop cage and let me take some
photos for an article I had hoped to do for the B5 Magazine. For those
who haven't seen it, the prop cage was like a wizard's cave of cool B5
stuff, basically every object that had been purchased or built from
scratch for the series, all crammed into shelf after shelf. And one of
the items that Dark Hoffman showed me was the over-thruster, which I
think had appeared as a piece of Whitestar debris in one episode. But
one of the guys told me that the object had been handed around to
other prop department guys on other shows and movies, who would then
do their best to work it into a shot. I think it was a private joke
amongst themselves, not really meant for anybody else.
You can read a list of properties (including Star Trek, B5 and others) that the prop has been used in