I just got freespace 2 and I'm loving it. I installed Freespace open and I think I'm going through the original freespace 1 campaign now. Only other space combat sim I ever played was freelancer. That said, in freespace do you ever get the chance to fly around and go where ever you want like you were able to in Freelancer?

Im afraid not.

awww man lol oh well, still one of the best games I've played. Oh, and I've been playing this with a mouse, is it better to use a joystick for it? if so, what's a good one to pick up?

That depends.
Even with the mouse set to maximum sensitivity, you still won't be able to make a 180 in mid-flight as quickly as you could with a joystick, or even the keyboard. Then again, a mouse is extremely useful for precise aiming. And, of course, everything changes depending on what kind of ship you're flying; for instance, the Ulysses is so maneuverable that sometimes even a mouse is too much, whereas the Ursa flies like a brick, and steers like one too, no matter what control configuration you're using.
Personally, I like to use the mouse, with my fingers on the Numpad of my keyboard in the event that I need to make a really, really sharp turn. That said, there's a certain visceral appeal to a joystick...

Uh, it would be good to be sure of what you're playing. What has happened so far?
People using joysticks tend to say that a joystick is absolutely necessary for FreeSpace. I'd like to disagree. I've played FreeSpace solely with a keyboard. I'd use the mouse if it worked like in Freelancer, but as it is, I just find the mouse control annoying. Keyboard has sufficed more than well and I don't plan on buying joysticks any time soon.
Though this naturally is a matter of opinion. It is completely up to the person to decide whether or not to use a joystick.

when i went off to college i left my joystick at home, but i picked up a logitech gamepad for $20...