I reply to all of them, because I really appreciate people who take the time to read and tell me what they thought of my episode. It probably helps that I don't have a ton of comments, so it's manageable for me.
I don't reply if I can't think of a response though. I prefer to respond by making jokes rather than just the usual thank you (although I do those as well)
I just think it's nice to show my readers that I appreciate them being there, you know? I always get so excited when someone comments on my work.