Chris:
I got tired of the rattles and high cost of replacing parts of the vanagon
skylight and removed mine.  I replaced with a manual sunroof which allows
opening front/rear/both or all the way out.  Although the purists scoff and
I'll likely never win a Concours De Elegans (sp?) Event, I am very happy
with the outcome.  The ventilation is very good, the sunroof keeps most the
rain out but is not as forgiving in that aspect as the skylight which had a
better overhang.  Living in Portland, Oregon, this was fairly important to
me and I've not yet had any problem with leakage when camping, either with
top up or down.
But by far the best part is being able to lie in the top bunk and look up
to see the stars.  The sunroof is right above our heads.

If you're interested, I have dealt with a guy out in Ohio who sells
aftermarket sunroofs for a now-closed-down company.  Very good values at
$65 a piece.  Install is a little tough in order to make sure you maintain
strength in the roof but definitely do-able.  I've got some pics on my
website (body / sunroof section) if you're interested.

Brent
http://www.weidefamily.net/vanagon/