So I was thinking of maybe getting into the Wing Commander games, but the only trouble is I know very little about them.

I am aware they use real footage with Mark Hamill and apparently have a really good story but, that's it really.

What is the best version to start with, what the controls like and how does it play?

Any advice would be appreciated thank you.

The best would be to start with the first three games but it must be said that the first two games have very primitive gameplay, the 3D world is sprite based and they suffer from severe slowdown with multiple ships on screen.
The stories of the games ain't that good to be honest but they are told in such a manner that is surprisingly effective and refreshing, this is also where the excellent artwork of the first two games shine and wouldn't be out of place in better indie titles coming out today.
Wing Commander III and IV use FMV with a decent cast (which counts as very good for mid nineties standards) and with the better 3D engine they are certainly worth playing today.
Wing Commander V, the story dissappoints, the FMV are more boring than entertaining IMO but the gameplay is top notch however, also liked the Giger-ish artwork done on enemy ships.

The spinoffs:
The most popular are the Privateer games though it must be said that Privateer 2: The Darkening was never intended to be a game set in the Wing Commander universe, you will have a hard time linking those two together.
Wing Commander Privateer however is a very good game, Elite like gameplay with an overarching storyline that made this game a really good addition to the Wing Commander universe and perhaps the best game in the franchise.
It also uses a sprite based 3D engine but here I didn't notice slowdowns and it also looks and plays better.
Wing Commander Academy is basically a storyless spacesim, it has been too long ago since I've played this and that was only a demo so I can't really say much about it, from what I remember it was choosing your ship and choose enemies and play.
Wing Commander Armada hasn't arrived on gog.com yet and I've also never played it.

Wether you will like these games or not, especially the core titles, depends a lot on how much you dig/can stand the
Hollywood interpretation of fighterpilot culture, altough it hasn't got the total idiocy of Top Gun it does have some of the naive sillyness that comes with older games and movies but thay may actually be a good thing.
If you seriously want to play these games I do recommend a joystick though.