What marcel said.
I have no practical experience using "full-frame" cameras such as Canon 5D, but it is generally acknowledged that photographing from a tripod is a must when desiring to fully utilize the resolution and quality of their large-resolution sensors.
Regarding optimal shooting aperture, you could also research lens test sites such as slrgear.com, where you can find quantitative measurements of lens resolution vs aperture (and focal length, for zooms). As marcel said, diffraction becomes a problem at large aperture values, however if you need large depth-of-field, this will not be so significant. Of course, you can defeat depth-of-field troubles if you use wideangle lens (if that is an option in your situation).
So, shoot from a tripod, then you are free to set ISO to the lowest possible value, which will again produce best results.
You can of course experiment in the field to find out what the practical limits are that matter to you.