I recommend that you make each plugin be a separate Eclipse project and that each plugin project be a Subversion project in its own right. In other words, make everything as independent of everything else as possible.
Subversion is a bit different from other version control systems, so it's certainly possible to have a master "plugins" project with sub-projects underneath it, for example. You'll probably find it easier if each of the sub-projects has the full SVN kit (branch, tags, and trunk) per-project. To check out and work with one of these sub-projects, you'd just use the SVN browser to select the trunk folder for the sub-project and instruct Eclipse to check it out as a project.
I also recommend using
Maven as a offline build platform for stuff like this, where you have lots of dependencies. Sometime's it's easier to be able to issue a single batch command that sets the whole thing in motion instead of racking up Frequent Mouser miles.
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.