Old thread, but in case someone else comes across this in a search:

None of the pop-in windows (rear or side triangles) had any evidence of sealant between the rubber gasket and the metal on my car. I'm working on a '74 164E, but it is very similar to the early 240 and 260. The only evidence of sealant from the factory was between the glass and the rubber gasket. The sealant was on one side of the edge of the glass only (the side facing out). Therefore, it appears to have been applied after the window is in place and installed in the vehicle. Using a caulk gun, insert the nozzle of the sealant tube inside the rubber gasket between the glass and rubber. Apply a small bead as you move the nozzle along the seal. The nozzle itself holds the gasket open as you pull it along. After the sealant dries (it never dries completely; just becomes less tacky), scrape off of the glass whatever oozed out of the gasket with a razor blade.

From the factory, only the bottom and sides of the glass had sealant. The top was clean. I used 3M Auto Body and Glazing Compound 08509. Advance Auto had it in stock for $27 in a standard caulk tube. Interestingly, I seem to have bought the last one, and they don't intend to restock. The Advance Auto website now says it isn't available and cannot be ordered. Amazon says 'unavailable'. 3M website says it is for commercial use only and not for individual sale...

An alternative might be C.R. Laurence CRL7708. It is thinner and designed to 'flow', so it might require a different application procedure.