The variations on the main theme, from the slow 2001: A Space Odyssey like opening for series one and two, to the insane rock stylings of the opening theme for the rest of the series. Not forgetting the catchy lyrics of the closing theme, unchanged since the first episode. The full length version at nearly 5 minutes long combines the original orchestral opening from the first two series and the closing theme, and includes the extra verse that wasn't in the show AND a fairly awesome bridge to tie both of the sections together!
"Tongue-tied" manages to be Music of Awesome and Crowning music of Funny! And, wow, can John-Jules strut!
The episode "Gunmen of the Apocalypse" gives the theme tune a western spin, resulting in one of the best and most spine-tinglingly awesome pieces in the history of Red Dwarf. The Western music plays whenever the Dwarfers are being badass and also at their Moment of Awesome at the end.
From "Queeg": There's a brief rendition of "Do Not Forsake Me, Oh My Darling", sung by Howard Goodall (who sang the chorus of the Rimmer Song and composed the theme tune) as Holly prepares for his showdown with the title character. It's only short, but it's incredibly well done. Here it is in all its glory.