The rules for Runequest III state that fatigue points are the total of the PC's STR + CON. A PC loses 1FP per round of combat or normal movement, and 2FP/round for more vigourous activity. Once FP's fall below zero, the PC loses 1% from all of his/her/its skills and resistance rolls for every further point lost, until he/she/it reaches a maximum negative of STR + CON, at which point the PC collapses. FP's are also lost by travelling (1FP/hour) , riding (1FP/90 mins), or by being knocked out or placed into shock (all FP's lost).
FP's are recovered at a rate of 1D3 - 1 per round of rest, which means that a completely exhausted character who has been travelling all day, mugged and beaten unconscious can be up and ready to run again after about four minutes of rest. This is silly.
So here's my idea:
PC's have two sets of fatigue points - let's call them first and second wind.
First Wind points are equal to CON, and are lost at the following rates:
Second Wind points are equal to the average of STR + CON, and are lost either as a result of the PC running out of First Wind points or from heavier physical activity not covered above - travelling, carrying heavy objects, a day's work at the Zebra Pens, etc.
Rates of loss should be left up to referees to decide, but I think that the standard rules for such activities should be inserted here, with some changes:
Travelling time is replaced by distance: