Are there any aspects of PhD work that do not translate well to distance learning? In another question about distance PhDs (Do any schools offer teaching or research assistantships via distance education?), I received several comments noting that PhDs on-line are of inferior quality to on-campus PhDs. If what is seen of PhD work from PHD Comics is accurate, PhD students seem to spend much time working independently. So, what aspect of a PhD cannot translate to the on-line format? What aspect of the process cannot be effectively conducted via E-mail or any of the other various forms of on-line communication?
A general answer is that a lot of PhD training is informal: it involves things that are taught by example, by osmosis, by noticing someone doing something wrong and correcting them (or right, and praising them). This kind of informal training is much more difficult in online interactions. Some examples are given below...

One specific aspect that does not translate well to online learning is the cross-pollination of ideas via proximity. 

A big part of training PhD students involves putting a bunch of smart, talented, hardworking people together and letting them learn from, motivate, support, and bounce ideas off one another. A prerequisite for this is proximity; you just can't have the same kind of interactions over email. Some research centers are explicitly designed to encourage this. At the Bell Labs facility in Murray Hill, NJ,


  Some of the hallways in the building were designed to be so long that to look down their length was to see the end disappear at a vanishing point. Traveling the hall’s length without encountering a number of acquaintances, problems, diversions and ideas was almost impossible. 


(Source: New York Times)

The research center I currently work in was built with a long hallway with this in mind, specifically to foster collaboration between students in different groups!

Another thing that does not translate well is learning scientific communication and mentoring skills. As a PhD student, I have many chances to practice speaking about my work to other graduate students, professors, and undergraduates. I also get to mentor M.S., B.S., and high school students in my lab. These skills are much more difficult to learn over distance. 

A third thing that does not work well over email and Skype is learning the etiquette and standards of the field. This is something that isn't explicitly taught (usually) but that students are expected to pick up by osmosis from spending time with other academics and others in their field.