Some of these are fairly obvious, such as the Elvis and Beatles references. Some, however, were so well-hidden that I didn't even notice them for years! Below are a few examples of the things I've spotted.
This one's a clear reference to the Beatles. In this episode of the comics General Pepper revealed Fox's past. When Fara asked why he didn't help Fox he explained that he "was just a Sergeant then." The picture is patterned after one on the REAL Beatles album, Sgt. Pepper's Lonely Hearts Club Band as I found out while looking through some old family records. The biggest difference is the comics say "Sgt. Pepper Happy Heart."
There's nothing like soaring over the skyscrapers of Corneria...Wait! What's this? A skyscraper has a gigantic "FX" logo on top of it! That's got to be the biggest Super FX ever!
The Awesome Black Hole of Star Fox became a graveyard of derelict spacecraft, and amidst the debris there appears to be...the Enterprise?
This one is debatable. Both Star Fox and this issue of Nintendo Power came out in 1993. As Fox McCloud traveled through the Awesome Black Hole he met a projection of his father's image, and amidst all of the circles in one panel there seems to be some that form "93" by Fox's father's ear. This seems a bit odd, but it's probably just coincidence.
This one's a bit obvious--just a typo that's pretty easy to spot. Fox should be calling him by his real name, not "Flippy."
In this episode of Mr. Itoh's comics, Herbert 2, Andross' android servant, was charged with cloning another Andross. The real Andross' final instructions and a copy of his brain wave patterns were encoded and stored on a Super NES cartridge, which Herbert 2 inserted into what looks like a Super NES!
A close look at the monitors in this picture reveals what appears to be three hidden references. A friend of mine, VanBrain, pointed out one looks like a reference to "CNN," and the "Amiga" and "NES" ones are pretty straightforward! Cool!
I really like Mr. Benimaru Itoh's style, particularly with the Star Fox comics, and it seems like his own signature is done in "Disney-fashion!"
Is it just me or does that sculptor bear more than a casual resemblance to Mario?