Without borders in my opinion. They wouldn't do much other than outline what's already been outlined by the background/foreground color differences. Unless I am mistaking what you mean by "with or without borders."
You can compare the pictures there. I took two screenshots of the same page with and without borders. The borders are the rounded boxes around each section and the sidebar.
I'm leaning toward no borders now. Twitter uses them, but I sometimes feel like they could go without. Imgur uses them, but they could probably go without too. I like how StackOverflow, Dribbble and GitHub do it. Very simple.
Without borders in my opinion. They wouldn't do much other than outline what's already been outlined by the background/foreground color differences. Unless I am mistaking what you mean by "with or without borders."