I had this EXACT problem on my 87. It used to be my mom's, and her solution wwas just to keep a plastic cup in the console and bail out the back seat
What happens, to the best of my knowledge, is that there is a little cover on each window that seals the gap in the outside gasket. Some idiot of an engineer designed it to be on the bottom of the window. Over time, the gasket shrinks, and the gap cover falls out. If there is a huge gap in each gasket with clean edges, this is your problem. You can probably find replacements from a knowledgeable VW mechanic. My fix, which gets rid of the standing water, was to head to Lowe's and buy some black silicone window caulk. Shield the window with a piece of paper (and/or roll the window all the way down; I left mine up because I knew some would stick to the glass no matter what) and fill the gaps. Let it cure, then remove the paper (you may have to cut it or wet it and just tear it off at the gasket level). Also, if this has been happening for some time, you may need to remove the inside door panel (they're little more than carpet-wrapped cardboard), de-mildew it, and line the non-carpeted side with some sheet plastic, since the factory door seal is without a doubt completely useless now. The inside will still be a bit damp after a rainstorm, but it's nothing that won't go away after a few sunny hours with the windows cracked.