If you are heavy and ride rough places now and then, stick to MTB 26" wheels.
If you ride more road, get ridgid forks. If you ride in a lot of really nasty wet environments get a hub gear rather than a cassette. (More trouble to fix a flat but less agro with mess and wear and tear, plus the chain line is always perfect so the loss of efficency by using a hub is gained, to some extent back by the great chain line)
I find 1.5" tyres to be the best, not too wide to slow you down, not too thin to sink into softish ground.
Dont skimp on parts or you will forever be adjusting them, get the best you can afford and cry only once, not each time you go up a hill and the fornicating things wont settle in properly
If your bike excepts it or you are building one up from parts (I reccomend this) get a front disk, and a rear if the frame will accept it. (Surly bikes make excellent frames that accept pretty much any compo of parts, they are steel too, so you get a nicer ride than alu)
There are millions of little quirky things, this is the cool thing about bikes. My bike is a real mongrel but its absolutely perfect for me. A great compromise of cost, weight and comfort. It will take a while to get right, but if you build it yourself (or have the shop do it) you will avaoid a lot of things that will make you think of upgrading.
You should be looking at about $600+ for a real dream of a ride. I know you can get stuff a lot cheaper but I guarantee that if you ride often you will soon want to swap out factory parts, its easier to just get it right the first time.
Here is my list if I was doing it again
Surly frame
Shimano Tiagra Chain wheel (Big cogs at the front)
Tiagra rear mech too
XT 9 spd shifters
Brooks B17 Saddle
AVID Ball Bearing Disk Breaks (BBDS)
Hand built 36 spoke triple butted wheels on decent hubs (Minimum Shimano XT) and Mavic rims
If you ride at night get a SON Dynohub built in (Sexy)