When talking about cars, There aren't many makers of transmissions, they all fall under a few umbrellas and few companies that build cars also actually engineer and develop them, most just buy one to drop into an application)
Borg-Warner,
Aisin (partner of toyota, but also a large supplier to GM, Mazda(Miata), Honda (S2000) and Chrysler (Jeep))
Honda,
Getrag,
Transmission Technologies Corporation(Tremec),
GM,
Mercedes-Benz,
Eaton,
Buhler Motors (Bought out Dana)
Magna,
Jatco (Nissan, formerly a joint venture of Nissan and Mazda, also bought out Mitsu's Diamondmatic spin off corp) and
ZF Friedrichshafen,
(Allison was mentioned earlier, but only makes commerical truck auto trannies)
The most impressive Manual trans is probably a Tremec 6060, it's a venerable Tremec/BorgWarner T56 strengthened to hold even higher levels of power. The T56 was in the C5 Vette, Viper (400-505hp versions) and Aston Martin V12 Vanquish(01-06). The 6060 is in everything from the 2010 CTS-V to ZR1 to 600hp Viper. It
so just so reliable, durable and flexible in so many applications. It's not the smoothest shifting, but it makes up for it in being a powerhouse, a real man's transmission.
Another competitor no longer in production is the Toyota Supra Twin Turbo Getrag 233-V160/161 6 speed, a trans so overengineered, that it could hold 1000+hp reliably over long periods of time with stock internals.
As for Sequential manuals, well gotta go with the Borg Warner DSG used in just about all VW and Audis, though not as technically impressive as the Ricardo DSG(a very minor, niche trans builder single or extremely low production vehicles) in Bugatti Veyrons and Audi R10/R15, it is cheaper, quick, a know quality and mass produced.
As for auto transmissions, the 8 speed Aisin-Warner AA80E that is everywhere in the Lexus line is very impressive, if you get over the "auto trans stigma" it is a very impressive transmission that can fit a variety of applications and function equally well while giving great fuel economy.