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If you lump together Squaresoft and Enix as one company, then I think it/they easily take the top spot.  It's not even close.  But if you count them as 2 (or even 3) different companies, then I'd say Capcom takes the top spot.  I'd put both Squaresoft and Enix, individually, as competitive with Capcom before they merged though.  Don't forget that in Japan, Enix was the most important third party for the whole 20th century.