I had left for another product, but now realize that GTD needs to be flexible to new situations and most "true" GTD products are not flexible.
I have had success using the task/subtask structure for projects. The parent task is tagged "project" and the subtasks are tagged "task". Using folders for projects eventually creates to much clutter as you cannot check off a folder as "done".
I have used OmniFocus, and while it has some great features, its lack of multi-platform offerings makes it hard to justify as your ubiquitous GTD tool.