Japan:
Matsumoku made many brands, including Aria, Vorg, and many more; they went out of business in the 80's and the factory allegedly burned down .
FujiGen Gakki still makes Ibanez and made Fenders.
Chushin Gakki made El Maya, Jackson & Charvel.
Tokai still have a Japanese operation.
Kasuga made guitars.
Teisco made budget guitars including Audition, Top Twenty, and other brands in the 60's and were taken over by Kawai.
I expect @Bassassin would be able to use his encyclopaedic knowledge to expand on the above!
In the US, Rickenbacker make Rickenbackers!