I stated taking pictures with a Nikonos 4, a 28mm Nikkor and a single Sea and Sea YS-60 strobe.
This outfit was cheap and sufficient to give me the bug. If I had my time again though, I'd have gone for a Nikonos 5 straight away. The Nikonos 4 O Ring is awkward to fit correctly and keep clean and the metering is not the best.
I soon replaced this with a Nikonos 5 and the fabulous UW-Nikkor 15mm glass. I still miss this combination for the fabulous optic - nothing in a dome port can produce the same effect.
I don't miss the constant worry of flooding though. Nik 5's have been described as the world's most expensive disposable camera. I only flooded one, and that was in a rinse tank. I think the problem is they rely on water pressure to hold the back firmly closed against the O ring. On the surface, the seal is not as tight. The moral of the story is be very careful when rinsing Nikonos 5s, and don't let them bang about in a rinse tank.
I progressed to a twin-SB105 setup with the Nikonos before changing to digital capture. A twin-strobe setup is well worth the expense in my view. Dark shadows are easy to get in underwater photos and there's very litle that photoshop can do to get rid of them.
All my digital shots up to now have been taken with a Nikon D70 in a Sea and Sea DX-D70 housing and twin YS-90 Auto strobes. I use 10.5, 12-24 and 60mm macro Nikkor lenses in a compact dome port, with an extension ring and zoom gear for the 12-24, and a standard flat port for the macro lens. I don't currently feel the need for a 105 macro but I'm sure I will soon enough.
I found this kit a complete revelation to use when I switched from film. A 2 GB compact flash will store 200 RAW files, with a little JPG as well for easy previewing. Battery life from the camera has been excellent and high capacity NiMH batteries in the strobes last longer than my air supply on most dives. I also found myself a lot less stressed about flooding. The Sea and Sea housing has a solid clamping system and a very user-friendly O ring system. I have a lot of faith in the engineering of them.
The big downside is the logistics. I transport my kit in 2 pelicases - one for the ports and accessories which goes in my dive bag, one handluggage size for the housing and strobes which carry on. I also wear a photographer's vest for the body and lenses and my wife gets the flight case with the laptop. It's not easy but it's possible.
I am currently waiting with much anticipation for my new DX-D200 housing to arrive!
I use the usual Photoshop software to process images. I use either that or DxO Optics Pro for raw conversion. The DxO software is a quick and easy way to correct for lens distortion and vignetting and is well worth a look, although PTLens does 80% of the job for about 3% of the cost, as long as you don't have a big batch to do.