Skype, Whatsapp, Twitter, LinkedIn are come to my mind (a few of my personal list), heck even Flash & Java Runtime (same problem different field). For the lack of better and popular alternative we have to stick with these. LinkedIn being on of the prime examples.
Twitter on the other hand has a different problem, solutions such as FriendFeed was a much better, almost by all means compared to Twitter (you could actually have a sensible conversation and while keeping almost all the benefits of Twitter) yet it didn't make people to switch from Twitter. Later acquired by Facebook, so I guess they succeeded.