To get back to the subject, the biggest missed opportunities are the same (biggest) ones missed in the Riff Raff Theater version.
Both Bruce Boxleitner and Peter Jurasik played major characters in the Babylon 5 series. Peter played a minor character in Tron, so there wasn't all that much opportunity to fit in riffs on Babylon 5 for that. But Bruce played the character Tron, and also played Capt. John Sheridan in Babylon 5. And in both, is character is apparently killed off only to come back to life. What seems a perfect riff to me would be to have some riffer pretend to say to Tron the exact lines said to Sheridan ("We thought you were dead"), and then have someone else pretend to be Bruce saying "I was, but I'm feeling better now".
To me, that's one kind of great riff. It's the kind which will be totally missed by someone who didn't already know Babylon 5, but fans of B5 would get it instantly. In was a riff like that which originally got me hooked on MST3k, many years ago. By "like that", I mean a riff that you couldn't possibly get unless you were already thinking of the movie that the riff-line referred to. I did get my hopes up a bit when the rifftrax-presents riff had one line about Babylon 5 fans (iirc), but IMO the main opportunity was missed.
Getting back to Peter, there could have been some simple "So Sheridan, we meet again", or "This time I'm not going to play with shadows!" line, especially if said with the exaggerated accent that Peter used when playing Londo Mollari. Or even a simple "VIR!!!" in Londo's accent.
(disclaimer: I've still only watched this rifftrax two times, and now that I've written these comments I'll probably find out that they did have riffs on Londo/Sheridan, and I was merely too slow to catch the references...)