I will agree with GUTS for the most part...
I don't know anything about the Neo Geo, so I've left it out of the following.
Graphically, the SNES has a larger color palette than the PC Engine/TurboGrafx and the Genesis. In fact, the Genesis has a very small color palette, around 61 colors on screen at a time. Because of this, I feel MOST Genesis games have not aged as well as their TurboGrafx and SNES counterparts. Games tended to have a "darker", less colorful and washed out look on the Genesis. The PC Engine/TG has a color palette somewhere in the 500 range, while the SNES is up there in the thousands. Rated this way, the SNES would probably be the top dog followed by the PCE/TG and then the Genesis.
HOWEVER, the SNES is slow as shit. The PCE/TG is quite a lot faster, as is the Genesis. When you factor these things together, the PCE/TG kind of gives you the best of both worlds (graphically) with colorful graphics, and fast processing. The Genesis is fast, but the graphics have a tendency to be more drab and unappealing to look at.
Here's a good example: I decided to whip out an old copy of Wonderboy III: Monster Lair for the Genesis the other day and give it a spin. I own the same game for my TurboGrafx. I had to shut off the Genesis version after only a couple levels. The game just looks so bad on the Genesis. The TG version has aged so much better and still looks good, today. I find this to be the case with many games released for both systems, but that's not to say there aren't some Genesis games that look really good. The Sonic games manage to look pretty bright and colorful, for example. But games on the PCE/TG are KNOWN for their bright, colorful look.
If you want to rate on available game library... SNES has the most, followed by the PCE and then the Genesis. Quality of games? I would rate the PCE at the top, but I am biased.
That's why I own a TurboGrafx. I feel the quality game to crap game ratio is better for the PCE/TG library than the other two. Owners of other systems may disagree: it's mostly a matter of personal taste. The PCE/TG library has some KILLER ports of arcade games that are hands-down better than their respective ports on the SNES and Genesis.
For me, it all comes down to the games. Technical specs aside, you should choose whether or not you want to buy a system based on the games you want to be able to play. Personally, from the 16-bit genre, I own both an SNES and a TurboGrafx. This means I have access to the two biggest game libraries from that era. My PCE/TG library is larger by a ratio of 10:1 over my SNES library. I also play my Turbo at least 4 out of 7 days of the week. I will play the SNES maybe 4 times a month. I own several versions of the same game for each system, and I usually tend towards my Turbo over the SNES most of the time. SF2: CE on the Turbo vs. SF2 Turbo on the SNES. I'll play the Turbo version 9 times out of 10 because I can use my TurboStick and because I like the Turbo synth music better than the SNES music. Graphically the games are virtually identical, but I suck at the game with the SNES controller.
I also now own some really badass SNK ports for the Turbo that were not nearly as good on the SNES or Genesis (World Heroes 2, the Fatal Fury games, etc). The thing about arcade ports on the PCE is that there are a lot of them, and they are usually very good.