Yep, 100px per grid works well for maptool, and it's easy enough to downsize to 50px which will run beautifully and will still look decent on a monitor. I know the standard for Dunjinni is 200px per 5' grid as that's geared towards printing as well as online play.

The important thing in maptool is to have an integer number of pixels per grid. That may seem obvious, but a number of published maps are printed having been resized which makes it tricky to get them to line up to a grid without a little editing.