Side-by-side diffs would be superior.
1) Do what Bitbucket does and have the side by side diff be a pop up window. I personally find this to be jarring and unnatural.
2) Combine both elements. It's what I do for my product. To better understand this take a look at
http://ny.testdrive.gitsense.com/index?#pid=22&cid=27&trail=
and switch to the side by side view. If you hover over the line number, you'll be able to see the diff line in unified mode below. With this setup they can provide side by side without having the user to constantly scroll left to right.
That said, I also want side-by-side diffs. They're necessary for more complex diffs.