my school has first semester all pass-fail, which is nice while you're taking it, and a real pain for applications! Some schools **cough cough Cornell ** require prereqs taken during the blanket pass-fail period to be "uncovered", or else they'll calculate it as a C, which sucks.
Most places are more flexible. I simply left pass-fail credits out of my GPA calculations, such that they neither counted for grade points nor for total credits. I did the same with APs - they're nice for credit requirements for graduation, but DO NOT factor into your GPA.
Things are complicated when you're at a system that uses either ABC scale (instead of 4.0), or a 1 credit-1 class system. For that, I was told by the schools and my registrar to count a one-credit class as 4 credits, a half-credit class as 2 credits, a double-credit class as 8 credits, etc.
Basically, Excel is your friend! Each school also will want their own prereqs calculated seperately, and some will want semester by semester calculations. Once you have all of your grades entered into a spreadsheet, you'll just have to work through those to pull out the stats needed for the specific school you're applying to.