An interesting article on keeping Twitter's Bootstrap code out of your HTML. I came across it while designing the CareerLog website. I especially liked his second point:
by hard-coding Bootstrap's class names into your HTML, you're marrying your code to Bootstrap.
In something as small as my CareerLog project, it may not be that big of a deal to go through and refactor a few template pages to use something else, but on larger projects, keeping the design and code separate will pay off in the long run.