One thing that revolutionized looking at medieval stained glass for me was using a serious zoom lens, and then spending time in post-processing really concentrating on the interlocking stories and symbolic images. Don't feel bad if you've walked into a bunch of churches on a tour and not really engaged with the windows, simply because they're too far away and too complex to really take in. Medieval pilgrims didn't have binoculars or zoom lenses, either. The clergy would have known the program of the images, or had records of their design, but the conventional academic wisdom is that the stories in the glass would generally awe the parishioners, inspire donors, and testify to the saint or saints who are in the stories that the church is faithful and supplicates to them.
North Rose Window
This is the view you rarely get to see. This is close enough for you to get a sense of what's depicted beyond a kaleidoscope of colors. Most of the major windows of the cathedral can be thought of as different aspects of Mary, who is the patron saint of the church. I learned recently that early churches dedicated to Mary were often on the site of an old (often Roman) fortification, with the idea that Mary as, pardon the pun, impregnable, would echo symbolically and sympathetically into the area. This window reads a lot like a modern organizational chart, except that authority is central and radiates out. Christ and Mary are enthroned at the center, and around them sit various old testament kings and prophets, and farther out events of the apocalypse (a kind of mission statement, if you will) are depicted.
If you want to really get an idea of how complex medieval stained glass was, head over to the jaw-dropping site, The Online Stained Glass Photographic Archive.
West Rose Window
The west rose window was constructed around 1225, but the view of it has been obscured by a massive pipe organ since 1730.
Coronation of the Queen of Heaven
Another Mary scene: This is her coronation as the Queen of Heaven. Note that the throne has architectural features which make it look like a cathedral, or a fortress--medieval thrones and seats of authority figures often make this point. The enthroned person rules over and from that architectural or symbolic point. Similarly (though not in the image), the many thousands of images of Baby Jesus sitting on the Mary's lap are a point about what Jesus rules over and from--mortal humanity. I don't know much of the theology behind the coronation of Mary theme, but I think it's about the highest point humanity can reach: the most submissive handmaiden gets the ultimate reward in heaven. I need to read more, because the fact that they share this throne (as in other images) as King and Queen intrigues me. She's not a wife-consort, and this is not the way monarchy worked, then or now. This is an exceptional gesture, and central to the doctrine, but I am unclear on what idea this sharing of a single throne implies.
Mary as Courtly Lady
Here's Mary as a courtly lady (although modestly dressed). She has that reversed S-curve posture women in gothic art usually have, signaling their shapeliness (I guess). She's carrying her prayer book and a scepter (with a fleur de lis top-piece). She's in a mandorla (which is constructed as though of interlocking pieces--very cool!), which marks her as emanating from the eternal realm. What's a little strange is that her attendant angels are swinging censers in a way that traverses that boundary, but I guess their allowed). The angels radiating around her circle are her own heavenly band, with a whole gamut of medieval musical instruments. I wonder about the one in the lower left, with his triangle, perhaps being drowned out by all the others. Maybe, he's thinking the equivalent of that famous SNL skit: "This needs more cowbell!" The other point I'd make about this is that it's quite the kaleidoscope of primary colors, which are carefully juxtaposed, with white and green for accents. Totally awesome.
Mary is often associated with the rose, but the lily is also a flower shown with her (especially in Annunciation scenes). In the photo above, it flanks the mini-rose window where she is courted by angels.