I always said Jen-too, watching a video they said Gen-too... it makes since, but really?

I have always called it JEN-too

http://en.wikipedia.org/wiki/Gentoo_Linux
The very first line.

I would say JEN-too, since that would be consistent with other words such as generation, general ...

--Ian

Exactly the same as the penguins of that name.

The only reason why pronunciation might differ would be if english wasn't your native language i.e. a dutch speaker might use a "gutteral" letter G (and no you have to hear it - it would be impossible to describe apart from sounding like you are "hawking your throat").

Or if your native tounge had a different sound for the double O at the end.

Hence I understand "jen 2" is correct (and yes I have been to the "south atlantic" and seen the penguins, along with macaroni's, kings, emperors, jackass and a couple of others).