I am looking bikes like the Specialized Rock Hopper 29er equipped with lots of gears for versatility and the ability to stand up to trail riding in places where tree roots loom large. What sort of bikes in this range stand out as good values that will be equal to this sort of duty?
While I have never owned one, I've heard from friends that 29ers are good for going over rougher or more technical terrain for xc riding.
When you say "lots of gears," though, you should be looking at which gears it has, not just that it has a lot of them. For example, on my full-suspension bike I have a 10-speed cassette (the rear gears) that is an 11-36t, which means that the smallest gear is 11 teeth and the biggest is 36 teeth. But when I was building my hardtail, I was choosing between a 9-speed cassette of 11-32t or 12-34t. See, the 11-32t means you can go faster, but the 12-34t means you're trading top speed for easier climbing. If you're doing more climbing, make sure the bike you're getting is geared for that. Or just get bigger legs.
Also you want to take note of the chainrings (front gears). You may find that you get duplication of speeds based on gear ratios. I'm running a 22/33/44 on my full-suspension and a 22/32/42 on my hardtail. Having 44 teeth on the largest chainring instead of 42 means that I have a higher top speed, but since I have a 44 and a 22, and my cassette has cogs that are 13t, 15t, 26t, and 30t, I get duplicate speeds that make it less than a 30-speed bike because 44/26=22/13 and 44/30=22/15.
As far as suspension goes, you'll want to check to see if the fork has adjustable travel and lockout. I don't have adjustable travel on either bike, but it's something to consider. As far as lockout goes, if you're riding xc, you gotta have it.
Consider brakes. I think disc brakes are awesome. I don't care much for rim brakes for mountain biking. You can look at these cool answers about mtb brakes for more about that.
For shifters, I'm a SRAM guy for mountain. I like the thumb-only shifters. Some people like Shimano. That's fine. Just don't get grip/twist shift.
With all those things taken into account, make sure to ride the bike before you buy it. If you get a bike on bikesdirect.com, you'll save some cash, but you may not fit on the bike. If you go to your lbs, you may be able to find the bike you want and the one that fits you. If you need a different stem or other component, they might even be able to swap the right one in for you and show you what's what on the bike. You really don't want to lay out a grand for a bike that won't even fit you properly.
So when you take these things into account, you can go to the manufacturers' websites and compare technical specifications to what you need and then find the lbs that's an authorized dealer. I think that's the best way to get the right bike.