-Is there a standard for the wires of the case and the connectors of MoBo, so that you really don't need to do anything else than plug them in?
Correct. Plug them in and you're done.
-My chassis fan has 4 wires, but the MoBo has only three pins for it. What's with that?
The 4th pin is for motherboard control of the fan, called PWM control. Some BIOS call it "smartfan" or something similar, basically it is a way for the user to control fan speed manually (e.g., setting it to "low") or automatically via pre-set temperature settings (e.g., if the temp is 50c, run at 1800RPM, if it is 30c run at 900RPM, etc. etc.). The 3 other pins are for power, and technically that is all you need for it to just "work."
Therefore a 4 pin fan
will work in a 3 pin power connector, but unless the motherboard features voltage control for the power, the fan will always run at full power without any "smart" fan control. I forget which 3 connections on the fan are the power and which one is for PWM (e.g., plug it on with the left one out or the right one out?) but just try it the other way if it does not work at first. It will work.
-The MoBo manual has two pins for the powerswitch, which are labeled "pwr" and "ground". This is probably really really stupid, but is the other one supposed to be a grounding wire (for safety)? How does the power switch work then with just one wire? (I have two indiscriminate wires coming from the power switch).
It's the same connector, just plug in the two pin case power connector to that and you're fine. Look at the case power connector, is it or colored? If it has a + and -, the - is the ground. If it is colored, the black or white cable is the ground and the colored one is the power. If it is not colored or labeled in any way... shame on the case designer for making a confusing power LED connector!
edit: duh, saw you already had your questions answered...oh well hope this helps someone!