I have a window like http://i55.photobucket.com/albums/g149/frogedude/HPIM16852.jpg. I fixed the rust area by grinding out the metal and welding in a new piece but now my concern is what would be the best sealant to seal up the windows?

I believe you only have two options. Urethane from a tube or buytl tape from a roll. Personally I find the butyl tape easy to use and cheap. I haven't used the urethane myself yet.

Buytl tape has always worked best IMO.