Of course, another sort of marginalia is the scholion. A Greek word, this, meaning a marginal note usually specifically intended to explain something to do with grammar or an obscure meaning. You find them throughout mediaeval manuscripts.
Sometimes, only the scholia are preserved, collected in separate scrolls (bear in mind that early mediaeval books were rolled up as scrolls, not bound volumes). This may lead to the curious situation where the original work is lost, but the commentary survives, giving us only a hint of the nature of the original work.