Growing the Beard: Generally acknowledged to have happened around the start of the second season, due to two factors: the writers now had a clearer idea of the series' setting and their depictions of the crew synched up better, and the first season finale had helped provide useful background and origin stories for the AH.com/CF.net vendetta. Nothing at all to do with Dave Howery's infamous beard.
Magnificent Bastard: The CF.net splits the role between Grimm Reaper, who talks the talk, and Ward, who walks the walk.
The Scrappy: Luakel, but subverted in that it is obvious that the writers have deliberately written him into this role.
Squick: So much. Oh, so much. Highlight if you dare: A teenager loses his virginity with the Gender Bendered evil Mirror Universe counterpart of a gay crewmember; that same gay crewmember is forced into a porn shoot with ten women; the details of Landshark and Iron Yuppie's relationship are so wrong that they can only be alluded to obliquely; and many more. A squick-worthy moment is usually denoted by most crewmen crying for 'the forks!' (to stab into their eyes and erase the memory of having seen the act), except Doctor What, who will muse that he finds it strangely arousing.
Even worse. In "The Narcissus Syndrome", Doctor What drinks a virus that changes his personality into something similar to DominusNovus and Super55. The result is a Doctor What that thinks himself as the most attractive person in the multiverse. He goes find the Mirror AH.com ship and has sex with his mirrorGender Benderedcounterpart. When he "wakes" from the virus influence, he cleans himself using several gallons of bleach, an entire toothpaste tube and a bucket full of medicinal alcohol.