Hi Wendy,
We actually just finished our basement a couple of weeks ago.
For my flooring I ended up going with something called "Cushion tile - aerobics flooring". It is sold at greatmats.com. I used to have foam puzzle mats over concrete in my basement and for me they just weren't enough. I felt like my feet and calves would sometimes hurt the day after doing high impact. The cushion tile was quite a bit more expensive (I think it was around $3 per square foot for the black color), but to me it has been so worth it. My feet have felt great since I got the new flooring. The only strange thing to me is that I am used to puzzle mats which are very quiet, the cushion tile does make some noise when I am jumping on it, but I guess I will get used to that in time. Greatmats will send you a free sample if you are interested in checking it out.
The other thing that I did that I am very happy with was putting straight edge tile mirrors ($8 for a box of six at Lowes, I think Home Depot may have them too) up on the wall that I face while I am exercising. Believe it or not I actually think I work harder and get a better workout in with these mirrors. No more slacking off for me :7
Have fun! You will love your new room.