Like a lot of other games on the system, Popful Mail on the PCE-CD is a dressed up older PC game with the core gameplay pretty much left alone. That's not necessarily always a bad thing, but it is the big difference between it and the Sega/MegaCD versions. There's a distinctive "generational" shift between the two in terms of gameplay. Though the PCE-CD version is quite playable and fun, the Mega/SegaCD versions are more enjoyably complex and stimulating IMHO. The original game is just too simple and same-y for its own good.
The Japanese MegaCD version is the best overall. The difficulty hasn't been "Working Designed" yet, so the enemies die quickly and you can take far more hits. The bosses are also waaaay more reasonable. It's a great kick-back-and-cruise kind of game.
The English SegaCD version turned out excellently in the translation department. The writing and the performances alike are great, particularly for the time. The characters are even a little bit more memorable than they are in the original Japanese. All in all, it's a fine example of localizing a "zany" anime/manga style.
If I had all the time and skills in the world, I would love to make a hack that combines the Japanese difficulty with the English translation.
The SNES version is not very fun. This is ironic, because it was made by Falcom themselves. It's only the second console game they ever made in-house...the first being Legend of Xanadu.
The PCE-CD version has beautiful portrait and cutscene art, no doubt about it. The bright colors are also nice. However, gameplay aside, what I really missed most from the MegaCD version when I played it was certain backgrounds. So many of the different sub-areas of the MegaCD versions have unique backgrounds while the PCE-CD version keeps recycling things. When you fight the boss of the second area of the MegaCD version, you can see this beautiful giant structure through a desert haze, and you realize that's where you're going next. I love moments like that in games. It's like that bridge in Darm tower in Ys, when you can look down on the town where you came from. But in the PCE-CD version, it's the same ol' background you've seen through the whole area. There's a lot of that kind of thing.