both Pronto and Pi were named after the screen names for two regulars on the series forum. Shep's visor resembles Geordi's from Star Trek: The Next Generation.
And the general uniforms for the Mallcop Command arc are effectively Next Generation command uniforms with the colors reversed.
And the events leading up to that strip involved a salute to David Drake's Hammer's Slammers: the mercenary unit Pranger's Bangers, led by Colonel Drake Pranger, whose head, Word Of God pointed out, is somewhat hammer-shaped.
There's a city on Celeschul called San Asimov. And a Port Weber is briefly mentioned.
Retired Rear Admiral Mikhail von Mauser. Stealthy until Thurl refers to him as "Mikki."
In this strip, Tailor says 'We're in a maze of twisty passages, all alike!', a reference to either Zork or Colossal Cave Adventure.
In this strip, Shlock gets put back together by jumping into a pod and reassembling. Once he gets out of the pod, he says "Whoa! I know kung fu," a reference to Neo in The Matrix.
Later an ex-Gav makes a point of saying he didn't say "I know kung-fu!" upon emerging from the Transmogrifier.