The technique Gooblah suggests with WB is correct to keep all the "settings" the same. What this does is re-run the map script. This means a completely new map will be generated. But all the "settings" such as map size, number of players, etc will be kept.
However, what MoenDVL requested is a little different: to keep the same terrain, but regenerate the resources. MqsTout also suggested regenerating the rivers.
I do not think there is any way to do that. In particular, all of the map scripts I know of perform the terrain generation and the river generation at the same time. So there is no convenient way to load one (terrain) and generate the other (river).
There are some scripts around which apparently read WB save files and convert them into python. I have never investigated them. I guess you could use this to save the terrain *and* the rivers, but not the resources.
If the goal is to do some kind of tournament where the map is fixed, you can do this by editing the WB save file, I guess. It is text, and well-documented. It is easy to edit this file with notepad and change which leaders are placed on the map. It would require a little more work to edit the starting units, so that civs without hunting don't get scouts, etc. But that may be close enough.
