I have the in-channel ones. They look/work the same except the don't have that little "lip" that goes around the top of them so they are a little more low profile as mentioned above. Also, there is no "glue" from the tape stuck to your paint, they seem to help the window close just a bit more snuggly at the top, and I believe they are less likely to get torn off in a drive through car wash (which I've taken mine through once a week or so for over 3 years). Some people say the stick on ones can get torn off in a car wash though I haven't actually heard of it happening with anyone on this board.
NOW, that being said. The in-channel ones only cover the rear window the length of the actual opening of the rear window so they stop right at the black upright channel which seperates the window itself from the small, non moving piece of glass.
The stick on outside ones cover the full length of the window AND small glass panel so they are about 3 inches longer.
Depends on which features/look you like. I happen to like the lower profile look myself.
One hint: 
If you get the Vent-Visor in channel ones, when you do the
rear window, there is a little tab on the rear most section where it butts against the upright channel. This tab is offset and has 3M tape on it. It goes
OUTSIDE the channel and sticks to the black upright. I've seen people try to stuff this INTO the channel and end up deforming the channel. When mounted, you don't even see this tab. It provides support to the rear of the visor.
Nicest thing about them is that in the summer at work I can leave the windows down almost an inch for ventilation and no one can see that they are open and all the parking lot grit doesn't seem to blow in. Now if it rains while I'm at work the inside stays dry.
If you squint real hard and get real close to your monitor you can just make out the little tab on the rear one I am talking about in the below image.

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My pics!!'03 Rennie w/all Tupperware
Custom Roof Basket
Mopar Tubular Brush Guard
Garmin GPS V & Laptop w/Nav software
RAM products laptop mount
Maglite w/mount
Rear cargo bay tool cabinet
AllJs Rear Shelf
Rear receiver
250k miles!
LOST #CR051230