On my website, which is a one-page JS site using Sammy.js and jQuery, when I middle-click a link with a mouse, the link opens in a new tab. But when I command-click on a Mac, it
There is some interesting insight here: https://groups.google.com/forum/#!msg/mozilla.dev.usability/H1qLTur4EFc/gXH007CAPk8J
Apparently the JS you are using can preventDefault() the cmd+click while the middle-click is unaffected. Consult the docs of your JS/Site framework.
preventDefault()