Depending on the trails you may be riding, you might want to rethink front suspension. Front suspension can take some of the jolts out of rough trails but it also adds a significant amount of weight which you might not appreciate when commuting. If you do get suspension make sure you can lock it out as it is really of no benefit on smooth paved surfaces. Within reason, you can learn to ride many recreational trails without suspension. If you decide that you really want to ride a lot of off road and technical trails, then you might want to consider getting a mountain bike in addition to a commuter/road bike.
If you are looking at riding "occassional trails" rather than hard offroad, you could look at a cyclocross or hybrid bike. You can get tires for either that are wider and more aggressive than road tires, but not nearly as fat and knobby as mountain bike tires. 700c wheels would be my first choice but there is really nothing wrong with 26" wheels. If you get into serious road riding you will likely notice a difference, but for pleasure/fitness/commuting, either size will suffice.
Though a bit heavier than aluminum, Ti or carbon fiber, chrome-moly steel give an excellent ride quality and is tough. It is also often less expensive than similar quality bikes in the same class in other frame materials. While you don't want to ride an anchor, don't get hung up on going as light as possible either. If you are a competitive racer, sure a few grams here and there can make the difference between first and second place, but for the vast majority of riders, you can save a lot of money staying with the mid-range component groups rather than the ultra-light professional components without sacrificing performance. That said, don't go the other direction getting a bottom end entry model unless you absolutely can't afford something a little better. Your budget of $1,000 is reasonable and can get you a good midrange new bike or a hell of a good used bike.
