For PCE, I'm going with Valis I. Gameplay may not be the greatest, but the game itself is just more ''Valisly'' then the rest if you can understand that. School girl goes solo against all odds. Music is great too. When I just want to relax and have some fun I could seriously play the first stage over and over and over lol.
For the entire series, I think I have to give it to the X68000 version of Valis II. The game has horrid controls, but once you get used to it's weirdness, the style and design is really awesome. Most especially the violence. The original computer versions of Valis II are gory, no holds barred, and depressing as hell. The console versions were really toned down in dark content and it really weakens the story imo. Watching the insane shit Yuko goes through in the uncensored II is quite eye opening.
I also have a softspot for the MSX version of Valis I. It is a terrible game in every category, but I don't know I still like to play it now and then. There is nothing good about it at all, but I still enjoy it....lol.