From personal experience I can say that lighting and floor are 2 of the biggest factors in how well a garage "works". Everything is hugely based on personal taste but here are my own thoughts:
If you're going for a showroom style garage, recessed lighting will go a very long way in giving it a modern look, and making it more a part of the house than just a cold, grimy work area. On the other hand, the cost is increased for recessed as you now have to cut holes in drywall, finish around the lights, etc. Many people including myself opt for fluorescent as it is a great bang for the buck, can be mounted anywhere, and provides good light output. If you find that your maintenance/work habits and styles change, you can't exactly move the recessed lights. Since I'm cheap I went with the "outdated" T12 fluorescent, mounted in 4' lengths, 2 bulbs to a fixture. I don't know what size your garage is but it would be a good idea to know how much area you're trying to light, and calculate the light output you need from there. If you're doing detailing I might recommend going with fluorescent as the recessed bulbs usually provide a very "focused" beam of light, which might make spotting imperfections in paint difficult. The T5, T5HO bulbs are more pricey than your run of the mill T12 but provide quite a bit more light.
Regarding the floor, again, it's a matter of personal preference, and choosing something that suits the type of work you'll be doing. Bare concrete is effective, strong, but will show scars and stains over time. Many people throw in the Racedeck tiles and love it - they provide a great texture and look, but don't have the muscle to stand up to repeated abuse of engine cranes, jack stands, floor jacks, etc. I don't know how in depth you get with maintenance but most fluid changes include some oil/grease dumped on the floor, and that can't easily be wiped up with racedeck. Your other options are epoxy/urethane style floor - those can stand up to abuse better but of course come with a higher initial price tag, along with tougher installation (as opposed to just snapping together tiles yourself).
In the end it's all really a matter of personal preference, cost, and knowing specifically what kind of work you do. The best idea is to hop on garagejournal.com and skim through the forums there - there are build threads like you wouldn't believe.