TubePopper is the latest to take on the video annotation space. It's a tough space to enter, as there are a number of video annotation tools already out there, some of which were out before YouTube's own annotate option for adding pop up messages within a given video clip. So far, TubePopper's main point of differentiation is its easy-to-use interface and additional feature options, such as more available colors for its speech bubbles.
It looks like TubePopper is also limited to the videos available on YouTube, though finding one to annotate is easy enough. Enter the URL for the YouTube video you'd like to annotate, or perform a YouTube video search directly on TubePopper's site. Beyond this, TubePopper has the expected networking features: embedding options, commenting, related clips, and one-click sharing across various social networks and bookmarking sites, which is a feature powered by Gigya.
Of course, even with all these features there's still one thing that YouTube and even Mojiti have that TubePopper is lacking--the videos created with YouTube annotate can be viewed on YouTube.