I have owned both. I currently own an 02 S281 SC and the engine is essentially a GT w/ the blower. The cobra engine is built to withstand abuse and higher levels of h/p. It is awesome. You see guys buying the whole car sometimes in the salvage auctions just so they can pull out that engine. I would also agree with 00s281sc368, it would be nice to have the best of both worlds w/ the cobra engine and the looks of a Saleen. Periodically you may see the 03-04 Cobra Saleens for sale, but with only 10 or so made each year, they're pretty hard to find.
Downside to the Cobra can be
suspension/handling, seats and relatively place-jane looks. The cobra broke loose on me a couple times taking turns while accelerating, barely ever happens in the Saleen. You can always lower the Cobra with some aftermarket springs to cut down on body roll. The racecraft
suspension on the Saleen really gives it the stiff race-car feel and great cornering, one of it's biggest selling-features if you ask me.
The seats in the Cobra are a friggin joke. If you take the turns too hard, you will end up either on the passenger side or in the back seat. The newer models have those two-tone suede seats that appear to have more lumbar support. I had a 96' and it just had GT seats with leather. When I went with the Saleen, I purposely sought the Recaro upgrade for that very reason.
The hoods on the 281sc's are composite. Not too sure about the 03-04 cobras. My car only has 13k miles and the thing is already cracking. Also, the latch is a piece of junk and cracking. Looks like my wing and side skirts are also coming loose (held on by Saleen's professionally designed double-sided tape, also available at home depot for $1.99).
Don't get me wrong, the Saleen is one awesome car. I truly enjoy driving it, and it has a more complete all-around high performance sports car feel. It's got the
suspension, the power, the interior upgrades, and definitely the looks.... Little things about the Cobra really stand out though, like the cloth top on the verts, the painted mirrors, and the leather shift boot instead of the vinyl p.o.s. in the Saleens (left over from the GT, with which the car came equipped when it was born at the Ford factory). I upgraded mine to leather with blue piping and blue stiching. way better.
Both cars get props, but the Saleen gets more looks. You just have to remember, as far as power, the Cobra is the king of the jungle in Mustang world unless you go for an s351 or s281-E (big price jump either way, normally).
One interesting thing I noticed is that most Saleen owners seem to like and admire the Cobra's. I don't think it goes vice-versa. The svt forums consistently bash Saleens as "nice cars, if you like bodykits and stickers...." I have to laugh at this, since obviously the car is so much more than that. Ultimately, they both have a lot to offer, depends on your taste.
Anyways, hope some of this helps. Either way, with the models and years you are looking at, you'll soon have a bad ass car for the right price...