I'm not that keen on the stock cross bars. My wife has a Thule rack that attaches to them. Once on an extended overlanding trip with some weight up there (Canyonlands Maze District) one of them bent and collapsed. She doubled them up after that - 4 cross bars. Then another time, even with all 4 bars she came down off a steep ledge and bumped the car pretty solidly (on Black Bear Pass) and all 4 cross bars let loose and the whole thing slid out the front, skipped off the hood, and landed down the trail a bit.
I put a Rola rack on mine, it's a little sleeker looking - nothing to grab or snag on trees sliding past (I've inadvertently used it as a 'slider' before - leaned the top over into a tree leaning over the trail). Instead of using the stock crossbars I just made some mounts using Unistrut sections from Home Depot. Cut them in sections, drilled some holes, bolted them into the channels, and bolted the rack to them. It seems a lot more solid and sturdy - if you really yank and shove on the rack the only thing that budges even a little is the roof itself. And it sits down closer to the roof so it looks less bulky. Here are some pics from an earlier thread:
http://www.toyota-4runner.org/3rd-gen-t4rs/173293-attaching-rola-roof-rack-2.html#post1748870
FWIW the Rola rack is pretty cheap, but mine did rust after a few years up on the roof. Last year I finally got fed up with it enough to take it off and spend a while wire wheeling ti and rattle canned it black again. Also, drilled some drain holes in the front and back ends of the rack where the bars droop downward, I found that in wet conditions they'd gather water, which would get rusty, then when you'd go wheeling and tilt the car into unusual positions, the water would come out of the ends and past the junction in the middle (it comes in 2 pieces) and pour rusty water down the side of the truck.
