Do you want a hard or soft cover?
For a soft cover, I highly recommend the AccessCover brand.
http://www.accesscover.com/
I had one on my truck for over 10 years and it held up perfectly.
On my new truck, I went with a hard cover. I looked around a lot and went with the Lomax cover.
http://www.agricover.com/lomax/ Extremely happy with it. It's a tri-fold but unlike others, you can pop it off very quickly when you don't want it. There's similar covers out there but I didn't like the ones that have drains in them where you need to run drain tubes through your bed (and drill holes through your truck bed).
You didn't mention what truck you have but if it doesn't already have it, I recommend you look at a tailgate seal. They're about $20 but do work well at keeping water and dust from coming into your bed around the tailgate.
Since we're spending all your money, also consider getting some bed lighting (that goes under the rails). With a tonneau cover in place, your bed light on the top of the cab is pretty much worthless.
For another level of cargo protection, when I know I'm driving in crappy conditions, I like to use hitch cargo bag similar to what's pictured below. These are large cargo bags normally used on one of those hitch racks but I put all my stuff in it and it rides in the bed of the truck.