Does it change when turning? Does it sound like it's coming from the front or rear? Can you feel vibration through the steering wheel or pedals? Is it wind noise, humming, airplane propeller noise, or something else? In another thread you mentioned you need brakes, and that can cause noise since the pads basically always drag slightly on the rotors. A stuck brake caliper could make things worse.
It wouldn't hurt to check and/or change the fluid in the T case and differentials. If the fluid in the rear diff is dark that seems to be normal. The fluid in the others usually seems to be a bit cleaner.
Jack the wheels up off the ground and try to move them left/right up/down to check for play, and see if they rotate freely. That can help you find bad wheel bearings and loose or worn suspension parts.
Try a grease with moly for the slide joints on the front and rear driveshafts (don't use it on the yokes). If it still clunks, check for loose or worn suspension parts or bushings, or maybe broken or warn parts that support the engine, transmission, differentials, T case (I don't think that's a common problem).
I currently have a loud humming that gets worst around 60-65mph that goes away when I turn slightly right. Signs point to a wheel bearing, but it could also be a CV joint, diff needle bearing, or gears inside the front diff. It comes from the front end and I feel vibration in the steering wheel. I need to investigate more.
I also have really bad wind noise from an incorrectly installed windshield. I put some caulk on it, which fixed it for a while, but I think that washed out at the carwash or blew away. My dilemma is should I pay to remount this pitted old windshield, or replace an almost perfectly good windshield with a new one. And do I need to have someone do something about the scratches on the roof that are rusting from the poor removal done by whoever put in this windshield.
Here is a thread about the humming.
http://www.toyota-4runner.org/4th-g...ing-noise-coming-front-end-while-driving.html