Actually... the SNES Ninja Gaiden Trilogy is a decent game to own, just don't pay too much for it. The real faults of it are the inferior music, and lacks of certain special effects (like parallaxing backgrounds). The color is deeper and things look a bit more detailed, but with the lack of certain effects, it's lost. The PCE version of NG1 is decent. Poor parallax effect, inferior tunes. Graphics however were pretty nice. My main complaints against the PCE version are: 1. Spinning swords doesn't work against bosses like it is supposed to. 2. Music isn't as catchy and fitting as the NES version. 3. Strange script differences. 4. Lack of certain effects from the NES.
Anyways, I highly recommend buying the 3 NES cartridges. Nothing is better. They are the ultimate versions, and no superior version is available nor will ever be. However if you have a PCE NG1, don't count it out. I'd love to aqquire it someday, just that it's rather pricey.