Nice. You're on a roll with the Civ4 art assets these days Deon.
If we're worried about natural resources crowding the map, just reduce their individual impact a bit. Make them provide less of an improvement to yields and happy and health bonuses through various buildings. I'm pretty sure you can alter things to make them appear more densely with a few changes, if I remember discussions in FfH a fair while back about their reagents resource never showing up.
It
does seem to be getting difficult to find some particular resources. On non-huge maps. The last game I played, I was disappointed to find there wasn't any Wheat on the whole planet. So the +25%

bonus in my sprawling capital from that Egyptian religious building I had went to waste. And I had to go to war a few times to secure a lot of resources that only had a single instance in the world. Lemons, silver, spices, silk, pigs and probably a few others. But then, all of those were probably wiped out by the millions-strong swarms of elephants ruling that version of Earth. Might not have had cavalry until well into the availability of Knights, but I was drowning in elephant riders.
Anyway, one of the natural resources that I would definately like to see is some kind of better wood, found in forests and jungles. Could give a bonus to the construction time of wood ships and siege weapons. Or let you construct a building that gives those units a promotion when built. Lumbermills come a bit late for that though. So perhaps you could also use a Camp, (To stand in for a logging camp) with a lesser yeild, and later upgade to a lumbermill. Wasn't there some kind of model for a wood resource around? Barring that, there's always the option to recolour and enlarge one of the existing tree models to make some kind of small grove to place in an existing forest.
And save some of those resource slots for the Future Era, Zappara. Deuterium pulled from ocean water or He3 harvested offworld. For fusion plants and fusion-powered units. Nanotubes to build the space elevator and some of the more outlandish units.
On generalstaff's ones for which he has no ideas:
-Nanobots are one of the easier ones. Required for building the Nanobot Cloud. And give a lot of the manufacturing buildings '+XX%

with Nanobots.' like they get with power.
-Pharmaceuticals (Or just call them medicines if they're introduced earlier) are a natural add for additional

in hospitals and the like. Or as a pre-req if it's available earlier. Spices are a good resource to base it off of, if it's an earlier thing. To simulate herbalistic origins. Though at that point you might want to make Spices just building it much faster, since they're sort of rare. If it's later then building a Pharmaceutical Company, or whatever, would likely require a chemical plant.