I'm going on 4 years with my Softopper so I thought I'd share some of my thoughts:
I have taken it through a handful of automatic washes and through Hurricane Irene ahead of North Carolina Task Force 1 with no problems. I have driven maybe ~110mph with it. (Downhill run out west: truck doesn't drive that fast.) Its basic design is sturdy.
I laced the doggy door shut using a hole punch and 550 cord. If you have the doggy door that is absolutely necessary if you are going to drive it through severe thunderstorms. I tried velcro on the vinyl first but summer heat melted the adhesive.
Although the top leaks less in severe weather than my previous Leer top, I built a plywood shelf with skids (72 x 40 inches) in the bed that pulls out. The shelf keeps everything elevated an inch or so off the bed and bone dry. It also helps me load and access items deep in the bed. The shelf has a lip to hold things on it as I pull it out.
I originally planned to replace the plastic brackets that hold the rear door bar in place with metal brackets. Instead, I incorporated step pegs on a cargo rack that also protect the brackets. (See picture.)
I had an overhead rack built from 1.5" square tube, with four removable cross bars and a platform on top for camping on the roof, and stake pockets on the side rails to extend the rack upward if necessary. The rack is half the weight of the only quality commercially available rack I found for this application (Kargo Master). I might still have the plans I drew if anyone is interested.
I trashed the bed clamps and screwed everything straight to my bedrails with sheetmetal screws. This keeps the aluminum base bars from bowing outward in the middle. The whole top fits and looks better now.
At time of purchase I elected to have a white panel sewn in on top instead of getting an all black Softopper. (You have to catch them at time of manufacture to do this.) The white panel makes it more comfortable for camping, since it keeps the temperature down, but it is a total PITA to keep clean. It currently has a lot of mildew staining on it that I need to clean off.
My fuel economy has suffered about 1 to 1.5 MPG with this setup. Interestingly, that loss was BEFORE the rack went on. The rack hasn't significantly impacted fuel economy.
The top offers little security for items in the bed and poor visibility, but you all know that. You buy it for its versatility, and hopefully you buy some stick-on convex side mirrors too.
My only major complaint is that the mesh and the vinyl windows are on two separate doors panels. This is a total PITA when traveling cross country through rain storms and camping in the back, when you need the functionality of both panels, but have to change the entire door out to either let the top breathe or protect your cargo. Softopper should really offer a 2-in-1 option.
Here are some pictures from Hell's Revenge trail in Moab and other parts of the West. Since these pictures, I have gusseted the front corners of the cargo rack and changed the rear bumper. Enjoy.