I wouldn't call a color change, and the N64 logo was for the system.

BTW, should we count the entire company's history, or just when they entered gaming?

Konami.

NOW:

edit: I was late >_>

capcom has, I know of at least 2 other logos, one red lettered, and the other white letters in a red block in the same font, both of which are different than the current font

but it has been the same for the past ~15 years or so

atari's has changed, plus atari hasn't been atari in forever to begin with

sega's has changed for over 40 years, It has been the same since 1968's missile command, but on the early 1968 Periscope it Sega's logo was different, red letters in a different font

Nintendo's logo has changed, it was a different font, on a banner for Sherif, and it was probably different during their pre-video game hears

Activision's actually has changed, but it reverted back to the original logo, for a while it had rainbow colors leading up to the a of Activision

Activision had changed their name to Mediagenic in the mid 80's, but I don't recall a logo.

I think Atlus is another...

Nintendo hasn't changed their logo, just use different colors for different packaging. The logo is still the same. In fact, here is the red logo used on recent game, you might recognize it.

This: