Hockey Puck Mouse: I could never feel how it was oriented. I know I'm not the only person who had this problem.
Earbuds: They fall out of my ears if I'm not completely still. I know I'm not the only person who has this problem.
iTunes: Great in 2001. Now it's bloated, slow, doesn't handle large libraries well, has terrible error messages (or none at all), movie rentals don't work, sync'ing works weird, the list goes on and on and on. I know I'm not the only person, again.
I would add OS X to the list in terms of usability as well. Take, for example, the 7-year long thread on Jeremy Zawodny's blog about focus-follows-mouse. Why couldn't they put an option in the mouse settings to allow focus-follows-mouse?