This site has many links to mapping software and online tools that help create presentations. There are also examples of how mapping is used in a professional and creative way.
Storymap: Another easy to use application that creates narratives out of maps--space to annotate and place images as well as show locations and movement on the maps itself.
Rumsey Maps Google Earth: Great maps stitched onto Google Earth. There is a big database of maps here and examples of warping.
Storymap for Images: This application allows you to take a historical map or any image and annotate it with links.
ThingLink (Florence Example): Another application like storymap--a bit easier to use but payment involved.
Neatline: Neatline combines maps and timelines. It is connected with the web authoring tool Omeka. Robust but with a learning curve. The quick start guide is here: http://libguides.richmond.edu/ld.php?content_id=10749496
Timeline JS: Timeline JS is really a tool for creating timelines ("cartographies of time" as Daniel Rosenberg and Anthony Grafton would say), but it is easier to use than Neatline and can be tied to maps.
Geojson Editor: Geojson is the geographer's version of Java script object notation (JSON). This editor allows you to make basic points, lines, and shapes, automatically writing the code as you go. A useful cheat and a good way to start learning the basics of geojson.
Enhancing the Desert: A Pattern Language for the Production of Space by Nicholas Bauch. Stanford University Press's first digital monograph as part of their digital publishing initiative. Maps photos of the Grand Canyon by Henry Peabody taken between 1899 and 1930 onto the canyon itself.
Konstantin Dierks's map of United States globalization--with interactive timeline.
ORBIS: The Stanford project for mapping travel times and trade in the Roman world
Photogrammar: A Yale project mapping photos taken by two government agencies from the Library of Congress between 1935 and 1945.
Ben Schmidt's discussion of his 2012 project on visualizing whaling routes.
Martin Waldseemüller's 1507 map made interactive by the Galileo Museum in Florence.