Even if the Apple iPad solves the problems of scale with digital maps, there is still the issue that annotating maps is far more difficult on a computer than on paper. But a handful of companies are creating applications that seek to alleviate this pain. One of the more interesting ones is Scribble Maps. Scribble Maps lets you draw on Google Maps and publish your drawings as jpegs, embedded (interactive) maps on a web page, or as KML layers that can be imported into Google Earth. In their pro version (currently in beta) you can also import geospatial data from shapefiles or spreadsheets, and manage your drawings in layers a la Photoshop.
Scribble Maps recently released this video that gives you a quick preview of what can be done with the software. Pretty cool stuff.