lukaszthegreat: How are they similar/different?
Other posts here have covered the differences pretty well, so I'll just add this tidbit. Just before GOG opened up I picked up X3, as it looked very likely. Then I snagged Freespace here.
In practice, I am having a very hard time getting "into" X3. The story is good, and then it just leaves you hanging. Badly. I'm not even sure where to go sometimes, so I get stuck. Freespace, on the other hand, also has a strong story but is more directed. Much more. The missions come, and you WILL do them. Period.
I won't call either approach 'better.' In theory, I would love to play in an unbound universe with X3, but in practice I don't know what to do and for all the manual detail, they don't really give you a lot of hints. So X3 winds up being frustrating.
Freespace, on the other hand, doesn't have any options. Your single-player choice is 'continue campaign', which is continue the story. If the difficulty is ramped, some of the missions are pretty hard. Fail, and you go nowhere. There's nothing you can do about it, so that's frustrating.
But having said both, I find myself clicking on Freespace more. I know eventually I'll beat the missions, where with X3 it may be literally years before I guess what I was supposed to do.
For the price, get both.