I've done a lot of research on this and the GT holds it's it's value better than most would expect. I know someone who has an M3 and that's what prompted us to see what the reality is.
Found 1,247 2006 GTs with average price of 20,003 (base 29,675), found 147 2006 M3s (base 56,600), average price 34,384. I'd say the stang wins that hands down.
Average price of 2001 GT was 10,281 and the 2001 M3 was 13,995.
We also checked GT500s, and if a person paid over sticker, there may an issue. The average price for a 2008 GT500 is 42,700 and I know someone that paid 65k. Of course, more time needs to pass before any judgement can be made.
2006 GT, FRPP drag pack, FRPP handling pack
2011 GT ordered 1/30, off the truck on 6/21
Black GT - 401a, Black/Cashmere interior
6 spd, spoiler delete, security package
3.73, HID, comfort package
Brembo brake package, Glass top
First mod - CS front fascia