If I were making this choice, I'd probably lean toward the LS1 car. I'm kinda GM biased; however, I did consider an 03-04 snake before I snapped to my senses and realized that I didnt want payments.
I've driven both cars in question, so here's some of my observations:
The Cobra has a very STIFF clutch...It's not something I'd really look forward to sitting in rush hour stop and go traffic in; HOWEVER, the car is so much fun to drive wide open, I'd deal with it. The blower whine is great and will DEFINITELY put a smile on your face every time you stomp the go pedal.
The F bods are decent daily drivers, but the clutches and rears could stand to be a bit stronger for the hardcore drag racer. I dont think that's a concern with the daily commute, but I've had a few friends break rear ends or have clutches stuck to the floor after running them hard at the track. Everything is repairable, and the rear on an F car is probably going to be cheaper than the IRS on the Snake (yes, one of my buds blew a rear on his 04 Cobra, so it can happen). LS1's make big power with simple mods, so with the money you save in the purchase price of the F car vs the Snake, you can easily build the F bod to negate any straight line peformance difference.
One thing I hate about the F cars is that stupid hump on the passenger side where the cat is. I think they should have put that somewhere else.
Depends on the car, condition and miles for me. I'd get the best car you can afford, no matter which model it is. Personally, if you're comparing a regular GT to a Z28 or T/A, I'd probably get the F car, but if it's an 03-04 Cobra we're talking about, then it'd be a hard choice for me.