I haven't upgraded to a 8.8 rear end & new gears yet but I've done lots of research on the subject. It seems like most people around this site tend to recommend 4.10 if your stang is an auto & 3.73 if you have a manual. The former is kind of a steep ratio so you'd definitely take a big hit on your mpg if you go with 4.10 on a manual.
The difference between the 2 is the amount of revolutions the cam makes for each full revolution of the wheel. The higher the ratio will get you into the powerband quicker coming off the line from full stop.
The consensus around here seems to be that 3.73 gears + t-loc paired with a manual trans provide a nice balance between performance & practicality for most daily drivers. Most will recommend 4.10 for an auto tranny. But ultimitely it just comes down to personal preference.
NOTE: Since you're upgrading your gears, you'll also want to get a custom tune to adjust your odometer to your new gear ratio. Otherwise, your tach will be accurate but your speedo will be off (possibly leading to speeding tickets).
Well, I hope this helps. Enjoy your new mods.