I once watched a co-worker completely bork a customer system by accidentally middle-clicking while moving his mouse after copying an ls -l of /usr/bin (where pretty much everything was a symlink to the real executables in /bin).
Yeah, he shouldn't have been logged in as root, but the point remains that middle-mouse paste can be extremely dangerous and fat-finger-prone.
I love Linux, but the cut and paste situation is really terrible. The middle mouse paste isn't a problem for me--it's that there are two separate "clipboard" buffers, which just causes all sorts of problems.
Shift+Insert has always been my preferred method of pasting into a terminal after too many mishaps with right-click or middle-click paste.
That problem has been solved by terminals whose readline awaits actual user input (actual enter from the keyboard) even when you paste a command with single line break or a multiline command. Most linux terminals do that nowadays, and it's also great for giving you a chance to review that oneliner you've copied from the browser, which could contain something different than what was shown.