so anyway, in no particular order, here are 9 of the best.
1. link / zelda

found on flickr, this incredible stained glass depiction of link from legend of zelda was created by lynda macrae of the glass house in ontario. the colours especially are stunning. see the original (and larger version) on flickr here.
2. einstein

this 60ft high tribute to einstein can be found at grace cathedral in san fransisco and was installed in 1964. according to the cathedral’s website, ‘einstein was chosen to represent natural science in a twelve-window nave clerestory series called human endeavor’. read more about the window here.
3. pyramid head / silent hill

pyramid head is a character from the silent hill video games and featured briefly in the apparently shite silent hill movie. this stained glass version of the pointer-headed cretin is actually pretty good though and was made by deviant art user laernath. for a larger version click here.
4. mega man

there doesn’t seem to be much written info relating to this mega man stained glass window but that doesn’t matter. it’s brilliant on its own. it was created by flickr user ‘gary in cleveland’ and some photos of the piece’s creation can be seen here. spotted at neatorama.
5. pixels

situated in cologne cathedral is this enormous pixellated window design, designed by gerhard richter and based on his painting entitled 4096 colors. according to wired, ‘richter devised a mathematical formula to systematically mix permutations of the three primary colors and gray’. impressive. photos from here and here.
6. electromagnetic spectrum

this huge piece is called ‘the electromagnetic spectrum in stained glass’ and can be found at the national air and space museum. according to the museum’s website it’s ‘a large stained-glass work showing the range of light that shines on Earth and how deeply it penetrates the atmosphere’. pretty geeky.
7. darth vader / star wars

i think this is my favourite of the bunch. found on flickr, this hyperrealistic verson of darth vader was created for flickr user axoplasm by a friend, based on an old christmas card. it’s extremely charming and would be extremely welcome in my flat. see the original on flickr here.
8. spiderman

artist chris roth made this beauty, entitled ‘introducing spiderman’, as part of a show in 2007 called ‘100 artists: a tribute to stan lee’. remarkably this was his first ever stained glass piece. read an interview with chris here and visit the artist’s website here for many more photos and info.
9. master chief / halo

a couple of years ago, jacob’s stained glass in buffalo, new york, created this stained glass window dominated by halo’s master chief. at first glance i actually thought it was a ninja turtle. then i realised he was holding guns. and he wasn’t wearing a shell. originally spotted at kotaku.
so there we have it. 9 great geeky pieces of stained glass and not one picture of jesus.
know of any more?