Speaking of John Gruber, he wrote about Markdown links today:
I know inline links
[like this](http://example.com/)are overwhelmingly more popular with Markdown users, but I personally much prefer the reference style for exactly the reason Quinn does. The inline style is easier, and I’d never argue against laziness as a virtue, but the reference style is just so much more readable.
I write exclusively in Markdown and with a few exceptions1, I use the “lazy” style of inline linking. I get the idea that writing Markdown links as if they were footnotes is more readable. It’s nice not to have long URLs in the middle of a sentence.
But when I’m writing, pasting in URLs as I’m typing not only matches the way it’s done in HTML, it also allows me to keep my writing flow as much as possible. I type the text, I paste the link, and I keep writing. Naming a link, moving down, adding a link line, and then returning up to where I was—it breaks the flow.
When I’m editing stories in Markdown, I also prefer to see the URLs inline because it allows me to verify that the right words are hyperlinked, and that they’re connected to the right URL. It’s easy to mess that stuff up. (Occasionally I even see Markdown leaking on Daring Fireball, due to a misnamed link reference.)
I’m glad Markdown does both, but I’m pretty dedicated to the inline link method.