I am looking for ANY software, other than adobe photoshop and its affiliates, which allows users to quickly annotate documents/pictures very easily. Furthermore, I need it to be able to save the document into its native form. For example, writing a remark on a picture and resaving it as a jpg.
You can try gimp http://www.gimp.org/ Code (markup): It's similar to photoshop (but free). Should provide what you need.
You may try iiCreator (http://www.iicreator.com) Its a Windows software which let you import JPG/GIF or shape files and export as a HTML5 interactive image map, You can add annotations including text, lines, with mouse-rollover effects and links. The final output are just few lines of HTML5 code which you can copy and paste to your websites, or blogs.
You could try Skitch. I'm not sure if it works on Windows (you're asking a bunch of graphic designers here, and we primarily use Macs), but I do know it is very useful for annotations, and I believe it's free, if I remember right.