I found the season to be pretty good (the only one besides Season 1 where I didn't find any episodes that I really dislike), with most episodes having small problems, but also having something to make up for them. However, if I had to choose a top 5 worst...
#5 - Tanks for the Memories: this episode did so many things right. Great humour, great Fluttershy, great song, great theme... And a terrible Rainbow Dash characterization, well, at least for me. I know many people love this episode, but I just think that Dash's stupidity should have at least some limits, though Cindy Morrow seems to think otherwise. Also, I noticed a funny thing - people who enjoy Testing, Testing, 1, 2, 3 tend to have some dislike towards this ep (including me), while the ones who hated TT123 adore this one. Hmm.
#4 - Castle Sweet Castle: not much to say about this one. The whole episode just feels boring, with very little of substance happening. The song is probably one of the worst in the entire series, the lyrics felt rather bland, and the constant chorus repeating was unasked for (it's ironic since I love True, True Friend). There was also that horriblte Sparity joke. Its saving graces? Well, the dynamic between characters is kinda nice, the finale is touching, plus I was glad to see some attention being paid to Twilight after Season 4 almost completely ignored her in most episodes.
#3 - Princess Spike: I love the scene where everypony helps Spike to rebuild the statue. It just feels so nice and heart-warming. But other than that, I found the episode to be pretty boring. The main problem, though, is the lesson Spike has to learn. It... doesn't have anything to do with the episode. Spike did get a bit carried away, but that just went nowhere. All the trouble in the end was caused not by him, but by dumbasses who organized this summit the way that some things went in the way of the other ones. I really hope we get some better Spike episodes in Season 6 (funnily enough, I really enjoyed Neal's next episode this season, "What About Discord?").
#2 - The One Where Pinkie Pie Knows: not much to say about this one either. Pinkie's characterization was okay, and some of the jokes were pretty funny, but the episode really dragged on for too long, especially considering it had such a simple set-up. Would've enjoyed it more if it lasted 11 minutes instead of 22.
#1 - Apploosa's Most Wanted: once again, Dave Polsky trolls the heck out of everyone. This time, he ignores how the basic concept of the cutie mark works and gives us a character who gets his mark without really understanding what he wants to do in life. Okay, Troubleshoose can be just a single defective case, I'll buy that excuse. But the final solution of his problem is what's really questionable. So he's gonna be a laughing stock for the rest of his live, still breaking stuff but being happy since he does get to take part in a rodeo? Uh, okay, I guess... The episode managed to get some chuckles out of me, plus it turns out to be connected with the Crusaders of the Lost Cutie Mark, so not a complete failure.