In marine aquariums in general, and reef aquariums in particular, lighting matters much more than it does in a freshwater aquarium. Photosynthetic organisms like coral depend on powerful lighting to survive. LEDs, the latest innovation in marine aquariums, can work in the same setups as fluorescents if used correctly.
The biggest drawbacks to LEDs is their cost. They're a new technology, so most plug-and-play models still cost more than standard fluorescents. However, reef aquariums may employ more advanced types of fluorescents, like T5 lights or powered compacts, so the gap between the costs is closer than it looks at first glance. Additionally, it costs much less to run LEDs because LEDs use less electricity than fluorescents. On top of this, fluorescent bulbs need to be replaced every six months, since they produce less light as they age. LED arrays may last more than 10 years without any detectable change in output or spectra. So the big difference in cost is up front.
The output of LEDs and fluorescents is also calculated in different ways. Traditionally, the amount of fluorescent lighting you need is calculated at 5 watts per gallon. This guideline does not take into account things like the depth of the tank. Since LEDs use so little electricity, comparing the amount of energy they consume doesn't tell you much. Instead, LED lights are rated by their output in photosynthetically active radiation, or PAR. It takes more work to calculate PAR, but most commercially available LEDs have a chart explaining the output on the box or in the instructions. So you need to do more research to figure out how many LED arrays you need to light your tank.
Ease of Use
Fluorescents, for the most part, are a tested technology. You purchase them at a pet shop, snap or screw the bulb in place and you're good to go. While plug-and-play LEDs have hit the market, DIY models still dominate the LED scene. Some do-it-yourself LED arrays have more features than their store-bought counterparts. So while LEDs can work just as well as fluorescents, it can take a lot more effort to get them up and running.
Does It Matter?
Most of these issues matter more for a reef aquarium than a saltwater fish-only tank. If you do not have any photosynthetic organisms in your aquarium, either lighting works just fine. A fish-only tank only needs enough light for you to see your fish. However, whichever type of lighting you use, you should put it on a timer to give your fish 10 to 12 hours of light a day, since most saltwater aquarium fish come from the tropics and are used to this much light per day.