Sorry for the hiatus ^_^;
So I recently bought a couple pairs of boxers from City Boxers. I've worn each a few times and I do enjoy them quite a bit. Being a poor grad student, I bought from their bargain section, which really gets you some great prices that beat most store prices even with shipping. Here is a photo of one of the pairs I got. The flannel is really soft and the material is very high quality :-) And they're all made in the USA, to boot!
An attribute I look for in a company I purchase from is an evident passion for the product they produce. You can clearly see it throughout their website, from the front page description of the company, to the made-to-order customizability of all their boxers, to the forums where the owner answers questions and responds to comments enthusiastically. I expect I will be a repeat customer.