Freetrack needs an active LED source pointing at the camera, while TrackIR works both ways. You can have active LEDs that the TrackIR camera tracks (just like Freetrack), or you can have reflectors that bounce back IR rays that the camera emmits towards you.
In the TrackIR software, there is a choice as to what kind of "target" to use. If you choose to use reflectors, there are 4 LEDs facing you on the TrackIR camera that light up, the radiation from which is bounced back by the reflectors. If you choose the trackclip pro, the 4 camera LEDs turn off and the active LEDs are 3, mounted on the clip that attaches to your headphones.
I prefer using Trackclip Pro, because it's easier and more comfortable to wear a thin set of headphones to attach it to, than wearing a cap with reflectors. In that sense, if resolution is comparable, i guess Freetrack is just as good a choice (ie, you don't lose much by lacking the option of having active LEDs mounted on the camera itself). My only gripe with Trackclip Pro is that it's too flimsy. Mine broke a mere 2-3 months after i bought my set and i have it fastened with duct tape ever since
I think a reasonably cheap and easy way to go would be to combine both. You could use a Freetrack modified camera as the tracker and buy a Trackclip pro to use as the emmiter.