Bow windows...
 

I have 3 windows on the bow of my boat that pop up and on one of them the actual window is coming out of the frame. What do you use to hold and seal the glass into its frame???

Most are installed new with a marine caulk/sealant. 3M has some real good ones available at most marine stores. Might want to stay away from the 5200 for this, if you ever need to remove them it will be a major PIA. The 3M 4200 might be a good choice.

3M's 4000 is like a silicone, stays flexible and is UV resistant if the sun will be shining on it. I used it to reseal my port windows.