I would definitely get the S tronic and at least the 170bhp 2.0ltr, I have the 2.0 ltr and I find it quite sluggish compared to my old 2.0 A4 avant - down to the weight I guess.
Options I would recommend would be: hill start, bluetooth, ipod connection - though you can get usb connector if you want to use a portable hard drive or other mp3 player), lighting pack (gives the car a bit of class, lots of led lights around the car), auto dipping lights - i didn't get this but wish i had. Sliding back seats - really useful as you can also tilt the back seats very slightly. I got the full climate control with separate control for driver and front passenger - my wife likes it hotter than me and it makes a difference, plus you get extra vents for the back seat passengers. I got the storage pack, and while it's not up to much i like having something under the seats than nothing at all, my previous audis used to have a pull out drawer which was much more useful.
Also heated seats are useful, I've used mine every morning from october through to april. I would love to have been able to afford the sat nav, but when I look at what my iphone can do for a couple of hundred ?s the audi sat nav is not as smart as it looks - though i suppose it doesn't have the advantage of 3g/wireless connection! The fact it can't do full Uk post codes is a bit of a deal breaker for me, that and the fact it doesn't get updated too often is not so good, but i'm sure there plenty of owners on this forum who would disagree - i'm just jealous I guess!!!!
Hope some of that was slightly useful, oh and don't forget privacy glass!