I loved the farmhouse episodes for several reasons:
1. "Within The Woods" borrowed a scene from the 1990 movie with Leo laying, comatose, in the bath tub. This was a reverse version (and the correct version) of the scene from the original movie. In the movie Raph was the one beaten up while Leo kept vigil over him while in the original comic book (and the 2003 series) it was the other way around. They also used April's narration as she writes in her journal which was also borrowed from the original comic and was also used in the 2003 series.
2. Several horror movie character references were made in these episodes including Jason Voorhees from Friday The 13th (Creep), Freddy Kruger from A Nightmare On Elm Street and Chop Top from The Texas Chainsaw Massacre 2 (the Dream Beavers and Berny and his chainsaw "The saw is family"), John Carpenter's The Thing (Mom Thing), and even Speed Demon was a sort of tongue-in-cheek reference to Steven King's Christine as well as a nod to the Mutato Heads from the original comic. I also thought that Bigfoot was a nice touch since I have an interest in cryptozoology as a hobby.
3. The final farmhouse episode, "Vision Quest", also contained a moment that was borrowed from the original movie, when Leo leads his brothers in a meditation session and they make contact with the spirit of Master Splinter, complete with the bonfire turning blue in his presence. The Deer Spirit was a nice touch there too.
4. Lest we forget the introduction of the Punk Frogs in the episode "The Croaking", which includes a pretty good re-imagining the frogs' origin as well as their appearance.
I've also always liked this arc in all of it's continuities because not only are the heroes usually shown going through the difficult recovery process following such a terrible defeat, but they also seem so out of place in Northampton. They have suddenly gone from steel, glass and concrete to trees, mountains and nature which can be a difficult sudden switch, especially when having to go to an environment that you are not used to.
Over all these are some of my favorite episodes in this series so far. Turtles In Space wasn't quite as good but City At War is shaping up pretty well. I'm keeping my fingers crossed for more good (down to earth) story arcs in the series.
I agree with your point, haven't seen any of season four yet though.