In SourceTree for Windows, you can right-click in the repository bookmarks window and select New Folder. This will create a folder and allow you to drag and drop repositories into to organize into groups.
In SourceTree for OS X, you can right-click in the bookmarks window and select New > Group to create a group which you can use to organize the repositories.
Both versions of SourceTree allow you to nest these folders/groups and expand or collapse them to show just the repositories you need.
On OSX, is there a way to open all the repositories in a group? I know in the Windows version of SourceTree I can easily switch between windows because they're listed on the left, but in OSX the bookmarks window is separate, so I have to switch to the bookmarks window before I can switch to another repository, making opening a whole bunch of repos at once a real chore.
Right click New > Group no longer appears to show up in OSX 10.12.3 in SourceTree 2.4.1 (97). However, it appears you can create a new Group by clicking + New Repository button at the top then selecting New Repository Group.
I certainly would like the New > Group right click selection back.