Pretty much everyone in the UK except Velocette. In the late 70's, all of Japan.inc made a 400 twin. Pretty much the same engine with minor differences such as the direction the balance shaft rotated and the shape of the valve cover. Even Singer made a vetical twin, but they set it sideways and gave it a shaft drive.
Some of the small players in Germany and Austria such as Puch made 2 stroke vertical twins, mostly with a shared combustion chamber.
In the US, most twins were of the V sort. This was largely because the roads were total crap in the early days of motorcycling and the narrower configuration was a big advantage. I think Cushman made some vetical twins, but I doubt any were used on 2 wheelers.
Wait, there was at least one vertical twin HD! In '42, someone converted a knucklehead to steam using a parallel twin from a Winton car because he got the minimal gas rationing card. This bike found its way to a museum/bike shop in Arcadia CA when I worked in that area. I even got to touch it, but they wouldn't stoke up the boiler and let anyone ride it.
