I just finished Bright Side of the Moon a while back and thought I would thrown in some constructive criticism about what I think would improve the next season.
1. Fix length trial and error puzzles
There is almost nothing more annoying than a lengthy trial and error puzzles. Typically these work well but a couple had way too much talking and cut scenes that they became frustrating. For me the biggest one was the finale to The Bright Side of the Moon. The constant change from each of the four sections was frustrating not because I couldn't figure it out but because of how long it took to go through each one. I eventually just broke down and looked up the solution because I didn't feel like wasting my time trying to figure it out. This also happened to me in the Midtown Cowboys puzzle which while funny became aggravating when it took me about fifteen trials to get the solution.
2. Change comments
For me it was annoying to have the first few episodes with the comments of everything to be exactaly the same. Perhaps in the future you could make the line different every episode or perhaps change the items that are selectable for comments.
3. Rename file names
This is something simple and small but for me it is annoying to have the episodes listed out of order in the program files because Windows sorts by filename. Perhaps if you could name the beginning of each file as Sam and Max-Episode X-Title of Episode. It's a small thing but to my organized mind it is really annoying. (In fact so much I went back and renamed them all! :p )
Other than that keep up the good work. I loved season 1 and am anticipating season 2.