Bad: nothing. I don't play games with bad plots if I can help it.

That out of the way:

Good:

Super Robot Wars (any title) - the creators take several giant robot shows, mash their storylines together and the end result is not only internally consistent, but awesome. Fans consider SRW titles as doing the included series' plots at least as good as the series themselves, and sometimes even better than the actual series. Gundam SEED Destiny, looking at you.

ICO, Shadow of the Colossus - the storyline is almost 100% showed, not told. And due to minimalistic approach, you have to figure most stuff out by your own rather than receiving answers in the game. But the world, design, and everything that happens is artistically BEAUTIFUL.

Okami - a course of Japanese mythology that's easy to approach by everyone, fun, quirky, amusing at times and moving in a powerful way at others.

Disgaea series - simply hilarious, but also touching emotionally when you least expect it.