There are many games that I feel arn't that linear. Most of them are large sandboxes where things happen, for example: Independence War 2 wasn't that linear. Besides the first star system, which was essentially a long tutorial, you could do things in any order, not do things, do extra things, and just mess around in a space ship if you wanted. The story does eventually coverge towards the ending, but it isn't exactly branching in the conventional sense. It's alot of random triggers, hints and "right place, right time".
A game that does branch and feel pretty linear is Mass Effect. Once you get command of the space ship, you can fly around space and do pretty much what you like. You don't have to stick to the story and can do other things, but you're basically stuck in a small sandbox mode until you move onto the next mission...