I'll never understand it when people say "I don't know how well this turned out." Does it look good to you? Does it look like what you're trying to represent? How can you expect to draw anything if you can't even decide whether or not what you're making is ugly/unrealistic or appealing/realistic? =P
In my opinion, they didn't turn out very well. I can tell what they are, but they look nothing like any stained glass windows I've ever seen:

The bright/saturated effects you're showing in your picture only show up when you're *inside* the building. From the outside, natural sunlight kind of takes over. Your windows feel more like in-set posters than glass, to me. Of course, pictures don't need to be realistic to be good. I don't find the style very appealing either, though. You should try to *suggest* details more, instead of just drawing every detail in. Right now you're like "well, this chuch is made of stone. Better draw *every single stone* on the church!", but if you look at some photos of churches, you'll see that stones blend together more or less in certain areas, depending how much the stones have eroded together and stuff. Lighten up some of those dark lines between the stones, and see how it looks.
Your glass windows seem to be somehow less reflective than the stone walls surrounding them, which is one of the main things giving them a very "painted wood" texture, instead of a stained glass texture. Just take a look at some photos, and good luck.