I'm mostly interested in what is the best way to protect the wood from bad weather, but any other advice on how to improve overall quality of work would be appreciated.
Scrape, then sand the wood well. You don't need to remove every last trace of old paint, but if you leave too much behind the new paint is liable to crack and flake quite quickly, especially if it's outside and the old paint isn't particularly clean.
I like to use a Skarsten scraper for this, there's plenty of alternative options, but I'd recommend leaving a power sander until last.
If you're renovating an old sash window and really want it to last, take the sashes out, remove the glass, and get them stripped. It's not so hard to re-glaze a window, smoothing the putty so it's neat is really very relaxing.
Then prime. I like to use a good quality aluminium-based primer, you can't afford to scrimp on this as it's the primer that really stops the weather getting to the wood. Use two coats, three if you're by the coast or have extreme weather where you live.
Undercoat next. Perhaps I'm a sucker for marketing ploys by manufacturers but I choose an undercoat from the same supplier and range as the top coat I'm going to use. A family member used to work in the paint business and they spend a great deal of time making sure the chemistry of the two components match.
Finally, top coat. Two coats, again, gives a proper depth of colour.
Last of all, keep a careful eye on the wood when you clean the windows. It really pays to make sure that the corners and the joints are sound, and if necessary a little touch-up each autumn helps.
if it's outside follow txwikinger's advice. If it's inside, it also depends what type of wood and whether you're going to paint it or stain it? If you're planning on staining a soft wood (e.g. pine) then you'll need to use wood conditioner to seal the grain and then stain (no need to use wood conditioner of hard woods, e.g. oak) after you stain it, you can use polyurethane for finish.