In Firefox, the "normal" way to open a link in a new tab is to middle-click on it. On systems without a middle mouse button (e.g. many laptops) this is impossible, so the replacement gesture is to instead control-click or command-click, depending on platform.
The problem is that there is a crucial difference between a true middle-click and a simulated middle-click. Normally pages can listen for middle-click events, but cannot prevent their default behaviour. This means that a true middle-click will always open a link in a new background tab. However, command-clicks don't get this special treatment, and consequently pages can and do prevent the click from having its usual effect, frustrating user expectations.
This is not just a theoretical concern. Gmail, for example, prevents the default behaviour of command-clicks, and instead opens the selected link in a new *foreground* tab. This makes it impossible to quickly open several links from a single message.
What I find strange is that on OS X, the equivalent gesture for simulating a right-click (using a control-click) does not suffer from the same problem. In fact, pages always see an OS X control-click as though it were a true right click, so they are unable to treat the two differently.
Is this something that should be fixed? I know that I personally find it very irritating.
TL;DR: Command-click sometimes works like a real middle-click, and sometimes doesn't. The two should always be the same.