There's a very simple fix for your problem... For resources, anyway.
Open up the Civ4BonusInfos XML file, and under each resource there's an <iTilesPer>~</iTilesPer> tag. What this does is change the appearance rate of each resource based on the number of tiles in its radius.
Be careful not to make the number too low, or you could have a massive overflow of a single (or sometimes multiple) resource(s). Try to balance all of them to achieve a realistic blend of resources... However, if you want to do things a certain way, do it however you see fit (such as a planet that's very rich in Copper and Iron, but has very little Coal).
In the end, it's really all trial and error.