Well you can sand off the primer, old finish, and old stain and then start from scratch.

As Hallett said and maybe just in that space paint the trim dark and the view will look like a piece of art.

If you really want them stained, then, get them stripped and sanded and restained. You wont be happy with gel stain since the graining wont show through, like it did before.

Patricia, I was thinking of a dark stain to hide the water stains. And I do think the contrast would be cool.

Are these new or old windows? If they're old, then staining them dark to hide the water stains is a temporary fix at best. The water will probably continue to leak and start the staining process all over again. More important would be to make sure they are water tight.

Diana, they are old windows--probably 40 years old. You're right, they probably need to be fixed, or replaced. There's condensation in them, too, so the seal is broken. I should have fixed this before doing the renovation, but didn't think of it!

If the seal is broken then get a new window and reframe with what ever you like.