Hello!

I'm not sure I can help with a lot of tools and links, but I can give you this:
- to achieve charting a medieval population and its living surroundings, I make use of this!: The Welsh Piper » Medieval Demographics Online ; it is quite simple to use and you can develop upon this tools to generate terrain and cities.
- talking about hexagon mapping make me think of Rolemaster Mapping System, which is a general and local map system dedicated to hexagon maps. According to dice-rolls and chart (Rolemaster ), you can easily draw continents borders and limits and then generate contents (taking account of surrounding features). But you should find a copy of RMS to get it.

That's all I can do for you!

Regards and have a nice time mapping!

Paul