Well Manufacturer's Championships only changes things, as there is none of that drivel in amateur motorsports.
According to Porsche, they have 14 World Titles for Makes or Teams.
That is seriously eclipsed by Ferrari however, whom have 16 F1 Constructor's Championships and 13 World Sports Car Championships, for 29 total World Titles according to Wiki.
Also according to Wiki though, Ford has 8 NASCAR Championships, 3 WRC Championships, 1 Sports Car Championship, and 2 Trans-Am titles (in the original era). Adding in the subsequent IMSA, Trans Am, and lesser victories (Koni, etc) plus John Force's 15? (I can't even remember anymore!), Glidden's 8?, Bernstein's handful, and on and on they would probably take the cake.
I would argue against Ford winning though, as many of those are not true "World" titles. You have to compete in more than one country (and morte than once) for it to be meaningful I think in this sense. So the original Trans Am (which raced in Canada a few times a year and Mexico) and Can-Am would apply, but NASCAR and NHRA certainly wouldn't.
So, if you are saying just major international ("global") championships, Ferrari. If you are saying all professional manufacturer championship's, Ford.