So, what's the scoop on Judy and Don? As early as "The Hungry Sea" (in a scene taken from the unaired pilot), we see Don kiss Judy's hand when she passes him a wrench. That is their first and only recorded kiss. John and Maureen wryly observe at the time that they can't very well ask her to play the field in their current situation, but seem otherwise to be happy enough with the relationship (if that is what it is).
About halfway through the first season, Judy wishes for a new dress and hairdo to impress Don in "Wish upon a Star." He is so impressed with the result that he downs tools and takes Judy for a stroll à deux. Later in the first season, in "The Space Croppers," Judy is quite possessive regarding Don when she sees Effra trying to charm him. Throughout the first season we are led to believe, I think it is fair to assume, that Judy and Don are "going together" or even "engaged to be engaged."
Other than the odd occasion in subsequent seasons when they are alone together, at least implicitly by design, or when they are working together (as in "Castles in the Sky") there seems little to support anything other than a casual relationship, but at the same time, there is nothing to suggest they have cooled whatever relationship they may have had. Judy and Don are obviously comfortable enough with each other to voice their disagreements (and they disagree most often about Dr. Smith), and that suggests to me that they do have a certain degree of secure emotional intimacy.
There are also several occasions where Don has to make a hasty apology when he fails to notice something new or different about Judy, so he obviously feels they are in a relationship. Near the end of the series' run in "Space Beauty" we see Don rely too much on this security when he implies that Judy could not win any beauty contest, resulting in her near-tragic win.
Perhaps the most interesting suggestion about their relationship, though, is barely visible on screen. If you look at the script for "The Keeper, Part 1," there is a stage direction near the end for Judy to wish everyone good night, then wink at Don and say "See you later," apparently also to Don. We never see the wink on screen (Marta Kristen's head is turned), but we have to wonder who the 'see you later' was aimed at. It's an odd (but not unthinkable) thing to say right after a general exchange of good nights all around.
Before moving on, let's consider where everyone slept. On only one occasion is it suggested that Judy and Penny share a room, albeit strongly. On a few more occasions, it is possible to think Penny has her own room. So my question is, was it Judy and Penny who doubled up, or... ?
It wasn't until the early '70's that the Mary Tyler Moore Show portrayed Mary Richards having a "gentleman friend" spend the night (and not on the couch either) and even that was handled so delicately that many staunch fans of the show missed the implication entirely. Given that Lost in Space aired a good seven or eight years earlier, it cannot be imagined that any suggestion of impropriety was intended by the scriptwriters, and yet, there it is, a wink at her special someone and a "See you later."