I conduct approximately 50% of my teaching on Skype, and have had hundreds of hours' experience with online teaching. I therefore have a vast array of tricks up my sleeve for getting the most out of this medium!
You may wish to check out my article on the benefits of online tutoring for full details.
At the start of each session I create a Google Document for the lesson, into which all the new vocabulary and grammar notes are entered. Students are provided with editing access, so that they can add to the notes and provide written answers to questions. They can either download their Google Documents and store them offline, or they can bookmark the link in their internet browser for revision later.
I also use screen sharing and instant messages to make the lessons engaging and interactive. This means I can use my mouse to highlight or draw attention to particular items on the page. Translation exercises and additional resources can be shared over email or via Skype, to supplement the work being done in the Google Document.
I have found online teaching and learning to be fun and very effective, and there are certain advantages which come only with Skype lessons. It is empowering to have instant digital notes from every lesson, which can be created more quickly and presented more clearly than handwritten notes; the notes can also be accessed easily at any time from any location, and are much harder to lose than paper notes! Sometimes my students opt for a combination of face-to-face and Skype lessons, to get the best of both worlds.