Unlike the author, when I was telecommuting I was never able to be effective while working in my pajamas.
When I would wake up I'd go down the hall to the office and read the first 5-10 new mails in my inbox to give me something to ponder while in the shower (that's where I get my best thinking done anyway).
I did the whole morning routine and put on clothes I could be seen outside in, and then back to the desk to work. For some reason, I would be more prone to goof off on the Internet instead of work if I had just fallen out of bed and parked myself at the desk for the day in my pajamas.