From the same episode as E-90 Super Sweeper (aka Thunderbird 2), the launch sequence for the new X-Tornado (the collapsible palm trees) is also a shout-out to Thunderbird 2's launch sequence from the puppet series.
Mothra and MOGUERA appear in Episode 48 on a mysterious island. Mothra's a bit more vicious-looking and antagonistic (a nod to her dark twin Battra) and MOGUERA is based on his Showa appearance and battles Sonic, Knuckles and Rouge at the climax of the episode. Godzilla also appears as a statue that Bokkun sits on for a minute before it crumbles apart when MOGUERA appears.
Chris' attempt to use the Martial Arts moves he learned between season 2 and 3 (and falling flat on his butt because he's been grown down to the age he was in season 2) is a reference to Dragon Ball GT and how Goku had similar problems.
Might be stretching it a bit, but during Episode 60 Chris and Cosmo watch the last report from a damaged space colony, with the reporter◊ on screen suspiciously resembling Kimba.
One popular sub used the same font that was used for the subtitles in Sonic Adventure DX.