I fish out of a WS Tarpon 160. A few years ago, it was the "it" boat for fishing--it is a very fast sit-on-top boat. It is also surprisingly stable--I can swim up to it in deep water and board it with no problem. I can also stand up in it, but I'm short and have decent balance.
Here are a couple pictures of my current boat--
And here is a picture of my prize catch from my kayak.
Since I caught this fish, I've also caught a 90 lb. tarpon from the kayak off Cocoa Beach. There is a small army of folks who fish for tarpon out of kayaks in the Tampa area. There is little that can match the thrill of sitting at water level while a 6' fish shakes and rattles in the air literally above you.
One of my buddies with a yak poon—

I used to fish from a sit-inside kayak. Here is a picture of my old boat.

The sit-inside had numerous drawbacks. It was hot. It was impossible to enter and exit the boat in water above thigh-deep. Additionally, they sink much more easily than a SOT, as the sit-in will fill with water if waves breach the cockpit whereas a SOT is essentially a sealed flotation device. Due to this, I had a good friend & tarpon fishing buddy from Sarasota sell his sit-inside boat because it filled up on him during a botched surf landing--he had to wait while his friends lifted his filled boat up. Finally, you don't give up speed in one of the newer SOT's as compared to a sit-inside unless the sit-inside is a racy touring model that really isn't suitable for fishing anyway.
The current "it" boats for yak fishing include the WS Tarpon 120, Tarpon 140, and the OK Prowler. These boats have supplanted the old favorites like the Tarpon 160 largely due to the presence of a tank well, which allows easier storage compared to the hatches (or my solution, a milk crate). Additionally, their smaller size makes them less cumbersome to handle out of the water without giving up much in the performance department.
Rigging options on both sit-insides and SOTs are limited only by the imagination, although I dare say there are more rigging options on a SOT because of the larger flat surfaces compared to most sit-insides. You can find lots of examples of rigged boats at http://www.paddle-fishing.com (there are also a lot of cool tarpon pictures at p-f.com) and http://www.paddlezone.net.