Cross-bars can be purchased for most vehicles that already include the rails. The cross-bars are usually very low-profile, and can stay on indefinitely. I bought a pair for my mom's Enclave.
On top of the cross-bars, you can do whatever you like. A wire mesh basket is nice and durable, lightweight, and you can put anything up there, from bags to firewood.
A hard hinged case is the best, if you want to lock stuff up there. I have a big Yakima Rocket box that I use a few times per year. Locks, is waterproof, hides valuables, doesn't really effect gas mileage.
The downfall to those big cases is that they're expensive, and you have to store them somewhere. I think I bought mine used for about $300.
They are a little heavy. It's not a lot of fun to put it on the vehicle by myself, but it can be done. A 4Runner or Pathfinder though, with that box, will not fit into a 7 ft overhead door.
Alternately, if you have a receiver hitch, you can buy a simple luggage rack for BEHIND your vehicle. they're mesh metal, and work good for coolers or big heavy-duty hinged totes, that you can lock. The downfall to them is, you have to remove whatever is on them, before you can open your hatch. But for a long road trip, they're great, and you don't have to climb up on the tires to load them.
My two cents...
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Yakima Rocket Box Pro 14 - great condition | Rock Haven, ND (bismanonline.com)
Cabela's TrailGear Cargo Carrier | Cabela's (cabelas.com)