IPEVO AnnotateIPEVO Annotate. This is a free download from IPEVO. It allows you to mark up anything that displays on your computer. You can also pop up a whiteboard to solve problems on.
You can also use IPEVO Annotator in Whiteboard mode. Here is a video to explain this.
For and ipad like experience, you can use a Wacom graphics tablet that comes with a pen. This will allow you to annotate with the pen and is much easier to draw equations with.