Poptops
Pop-tops are the ultimate camper accessory. Sitting low to the roof of your vehicle when not in use, they don't affect fuel consumption or access to low areas like a high-top does; when parked, simply turn the latches, push up, and you have instant headroom and natural light. Most, if not all, pop-tops can also include a bed.
As far as I know, there are a few ways to get a pop-top installed onto your van:
Sportsmobile
Sportsmobile are a well-known Ford and Chevy converter, making customized vans for overland adventure. They'll also install just a pop-top into your existing van, for $5000 to $6000. Ford vans can be regular body or extended, 1992 and newer; Chevrolet vans must be 1994 and up. 2007+ RB low-roof Sprinters can also be fitted with pop-tops.
The optional bed in the pop-top (or 'Penthouse Top') is relatively small - 41" wide by 76" long. There's an extra six inches all around for 'elbow and leg room' but it's not part of the padded mattress. Still, two can sleep comfortably up top. The top itself is strong, and the conversion (according to Sportsmobile) actually strengthens the roof!
Electric lift is an available option, as is solar prewire (the wires are built into the top and fed into a body pillar inside). Electric lift tops can carry up to 150lbs of gear on the top, and still be raised and lowered; Sportsmobile recommends no more than 40lbs on manual lift tops.
With the top popped, there's 6' 10" of headroom (8' in the Sprinter).
http://www.sportsmobile.com/1_penthouse-top.html
GTRV
Located outside of Vancouver, BC, GTRV (aka Coast Outfitters) do full conversions as well as partial - including installing poptops on a range of vans. I've seen Ford and Chevy fullsize vans, as well as Astro/Safari vans, Toyota Siennas, and Ford Aerostars.
Tops come in angle-rise versions (V-tops) or straight-up pops (T-tops) and are low-profile - hence the GTRV label: Garageable Top RV.
Prices are similar or slightly higher than Sportsmobile, the last I heard (ie. $8000+). Their customers rave about the quality of work, and the pictures that I've seen of recent conversions back that up.
Colorado Camper Van
I don't know too much about CCV. The owner of the company built his own poptop, shown below, and since then has started his own company doing van conversions.
The build was documented on expeditionportal.com: http://www.expeditionportal.com/forum/showthread.php?t=23254
The website says that they can convert any type of van - not sure if this includes a poptop or not, nor do I have info on prices.
He also offers a top bunk solution for $2400:
These pictures are taken from the Colorado Camper Van site.
http://www.coloradocampervan.com
Ursa Minor ECamper
A pop-top for a Honda Element! No cutting - it uses the sunroof as access.
http://www.ursaminorvehicles.com/camper.htm
GR Travel Tops
(Located in South Africa)
More akin to a roof-top tent than what we typically imagine a pop-top to be, the GR Travel Top opens up and folds out to the side. This gives maximum headroom at all times, since the bed sets up in the fold-out section to the side.
Apparently, the travel top can be modified to fit most vehicles. There are pictures of completed installations on Jeep Cherokees, Land Rovers, Land Cruisers, and various single and double cab pickups. In some of these applications, the 'top' includes a build-out of the pickup bed, creating amazing space, with built-in cabinets, and apparently the possibility of additional bunkbeds. These latter applications are more like camper shells, and not truly pop-tops. But the Jeep Cherokee install below at least looks like a proper pop-top.
No info on price at this time, or whether these can be shipped and installed outside of the factory.
http://www.grtraveltops.com/index.html
More pics of the top on a Toyota pickup here:
http://www.cruisers4sale.co.za/Images.aspx
Other conversions
Those listed above are the only companies I know of that will fit pop-tops to your own van/jeep. There are other conversion outfits that will include a pop-top in a new conversion out of the factory - Pleasureway in Canada has the Traverse on the Ford van chassis, for example, and Safari Condo has a number of different tops available. There are also pop-top camper inserts for pickups, which I don't cover here.
Cool, but unavailable
American Expedition Vehicles has a sweet looking pop-top concept for a Jeep Wrangler:
Build Your Own
Only for the very brave! Building your own pop-top is a hefty undertaking - that first cut into the roof of your beloved van must bring your heart into your mouth! Still, some have attempted it, and some have even accomplished the feat! A few of these projects are listed below. Given the price of pop-top installation from the companies above, you could save some serious money by installing your own top.
Using an old VW mechanism
A guy from the Sportsmobile forum found an old VW pop-top mechanism at the junk yard. He combined it with a slice of an old fiberglass high-top and installed it onto his Ford van. The full thread (including pictures of his incredible self-built interior) is at http://www.sportsmobileforum.com/viewtopic.php?f=24&t=2650.