Well, I've really slowed down reading these, I have up to episode 23 read, but here are my favorites so far:
I really enjoyed the first two episodes, "The Recruit," and the "Workforce." I also really liked episode 11, "The Unkillable Thread," due to the fun ways in which the thread killers tried to kill the thread. In Season 2, "The Greatest Journal" was a fun one, because it didn't follow the normal layout of an episode, it was more just showing some personality of the characters. I really liked the setup of "Speaking Term," where instead of taking place in the office, it took place mostly on The Johnny Fiama Show. "Dontcha Just Love Holidays?" was also a favorite, I really liked the idea of the holiday themed episode. I can't wait to finish Season 2 and start season 3, which I hear is a really great season.
I feel really lucky that I found this whole series to start out with. I had seen the Thread Killers Organization mentioned a few times on the forum before, and I didn't really know (or care) what it was, and didn't feel like looking it up. Then I saw that it's thread was recently edited, so I checked it out and read the pilot (which by the way I also loved) and then I started looking for the episodes to start reading. If I never clicked on the thread that day, I may have never found it.
So, still really enjoying these, and can't wait to read further in the series. You did a great job!