Well first, here's the succinct version of my reaction to "Marooned":
Okay. This episode's gonna make you cry. A lot. (If it doesn't I want nothing to do with you.) Let's try to discuss it without breaking down again.
One of the main reasons why I have such nostalgia for Jim Henson's productions where so many other shows I watched as a child are forgotten is this: the Muppeteers weren't shy about making their young audience feel ways about stuff. The Muppets could go to some pretty unexpectedly sad places as discussed here, and there were moments in "The Muppet Show" that blindsided and haunted me both as a child and as an adult with their open poignancy. It certainly helps that, above all things, the Muppets are sincere. "They are vain and hopeful, selfish and generous, complicated and true," wrote Roger Ebert in his review of "The Muppet Movie", and this quote has stuck with me forever because it is dead on, "They mirror ourselves, except that they're a little nicer."
So what we have here in "Marooned", which many "Fraggle Rock" fans agree may be the best episode of the first season and perhaps the finest episode of the entire series, is essentially a bottle episode (of the Trapped in a Freezer subtype). And it is a character development episode, as so many bottle episodes are. And, again, like many bottle episodes do, the two characters being developed here are two characters who haven't had much to do with each-other and don't seem at first glance to have anything in common.
But Great Gorg is this one effective. And for me the reason is this: the two characters trapped by a cave-in here are Red and Boober. At this point in the series, we don't know much about either character. Boober serves as kind of a foil to the other Fraggles; while other Fraggles don't seem to worry about anything, Boober worries about everything. The only thing he seems to have a grip on is laundry; it's the thing he's in charge of, so it's the only thing he feels he has control of in his life. And as for Red... well, I'll discuss her in more detail in a future episode review. But right now, we know that she's a very active wild child who has some insecurities carefully buried deep inside.
In short, we have two characters here who, I just realized here, kind of personify two very different reactions to anxiety. You can either let it control your life, or bury it deep within you to save face -- but also make it all the more intense when it does break out. When Red and Boober find this common ground, it's incredibly moving. The song they sing together during this moment is haunting. People, this is up there with "Feed the Kitty", the "Married Life" sequence in "Up", the "Souls don't die" scene in "Iron Giant", and the flower scene in "Brave Little Toaster" in terms of, "You can gauge whether you raised your kids right based on their reaction to this."
(I'd be remiss if I did not mention that this episode also has one of the most downright adorable Doc and Sprocket B-plots.)