What is the best way to prepare walls, windows and baseboard for re-painting
Painting is easy - preparing for a new coat of paint so it will last is the hard work.

You should scrape off all loose or peeling paint - otherwise the new paint will simply peel right off there. Only after that should you move to spackle and sanding to prepare the base for new paint. On wood items "putty" is preferred over "spackle" which is more of a drywall/plaster repair item, though it's somewhat irrelevant when it's being painted over.

The window looks like you should investigate for and fix a leak. If it gets that wet, new paint won't stick either. 

The dark spot in the second picture is in the same place on all the pictures so it's a camera defect, I guess - at first it looked like mold.

The blisters in the third - more leakage? Or pitch bubbling out of the wood?