Currently I ride a Trek 7500 hybrid to work. I pretty much hate the riding position of the hybrid, and really like riding in the hoods of my road-bike. I don't want to take my expensive road-bike to work with me, but I am getting sick of the Trek. I just got a bonus at work, so I'm thinking about getting some kind of road-bike for my ride to work. I'm thinking of something in the <= $1000 range. I'm mostly concerned about making sure the rear rack is far enough back that I don't have heel-clearence problems. My trek is just barely long enough. I'm sure there will be lots of suggestions to get a trek 520, but what else is out there in this price-range with an extra-long chainstay?

Forgot to add...I will occasionally be riding on a rail-trail with gravel, and will use this for a few 80-100 miles day-trips also. Primary use will still be commute to-from work on flat/windy 5 mile route.

Nashbar has a touring frame on sale. You could build it up. It has been tempting me lately but I won't be doing any touring for awhile and I think I will0 pass for a few years until the kids are a bit older.

Surly Cross-Check is a good option. Can usually be bought as a complete bike for $800-900.

I have a Surly in a 58cm frame, 47 shoe size, Blackburn Expedition rack with Arkel T-42 panniers and have absolutely no heel clearance problems. It came with 700x32 Ritchey Cross tires, but I changed it out to 700x28 Specialized Armadillos. No problems at all running it on gravel trails. Very comfy on longer rides - I have a 25 mile round-trip commute, and have used it on a 50 mile ride with no issues whatsoever.

Perhaps you should look into a cyclocross bike. It would certainly meet your requirements, road bike handling & trail work will be a cinch!

Bianchi Volpe

I'll toss in another vote for the Surly Cross Check. I don't have one, but have a good friend that does. Super high value and super versatile bike. It's what I will replace my touring frame with when it dies.

A cx style bike will be a bit more agile than a Trek 520, but just as practical on a commute. See also Jamis, Bianchi, Fuji for good value cx/touring style bikes.