I stumbled upon this pile of station maps in my crawl of tokyometro.jp. I had my file manager sort them by size, which to my delight sorted them from least- to most-complex. Here they are all on one page.
The maps were re-sorted on 2015-07-26. I first put this up in 2013, but noticed in 2015 that Shibuya Station needed to be in position #1 (at the very bottom) instead of #23.
Shibuya Station notably features an underground river that inhibited some further construction.
Note: a few maps are duplicated because they connected underground, e.g. Hibiya/Yūrakuchō.
kita-ayase
hon-komagome
todaimae
nakano-fujimicho
shin-otsuka
ochanomizu
shimo
kodemmacho
nezu
shinjuku-gyoemmae
shin-nakano
minami-asagaya
shin-koenji
heiwadai
gyotoku
iriya
meguro
kanda
chikatetsu-akatsuka
honancho
sakuradamon
myoden
nishigahara
nishi-kasai
minami-sunamachi
inaricho
sendagi
suehirocho
myogadani
hikawadai
machiya
hiro-o
kagurazaka
ebisu
akabane-iwabuchi
ayase
gaiemmae
senkawa
toyocho
wakoshi
nakano-shimbashi
ochiai
shin-kiba
yoyogi-koen
kasai
shirokanedai
oji-kamiya
waseda
minowa
nogizaka
tatsumi
tsukiji
higashi-koenji
yoyogi-uehara
yushima
naka-meguro
edogawabashi
tawaramachi
kotake-mukaihara
yotsuya-sanchome
tokyo
minami-gyotoku
hanzomon
baraki-nakayama
kyobashi
gokokuji
higashi-ikebukuro
komagome
nishi-nippori
hatchobori
zoshigaya
ogikubo
chikatetsu-narimasu
kita-sando
nijubashimae
oji
kamiyacho
shirokane-takanawa
takebashi
nishi-shinjuku
nishi-waseda
minami-senju
roppongi-itchome
suitengumae
urayasu
kiba
toranomon
kinshicho
akasaka
kojimachi
azabu-juban
takadanobaba
shintomicho
tsukishima
nakano
ginza-itchome
yotsuya
kanamecho
nakano-sakaue
sumiyoshi
toyosu
higashi-shinjuku
ningyocho
kiyosumi-shirakawa
asakusa
hongo-sanchome
shimbashi
nishi-funabashi
roppongi
monzen-nakacho
higashi-ginza
kayabacho
oshiage
akihabara
mitsukoshimae
meiji-jingumae
jimbocho
ueno
ichigaya
ueno-hirokoji
naka-okachimachi
omote-sando
korakuen
kudanshita
shin-ochanomizu
awajicho
nihombashi
shinjuku
tameike-sanno
kokkai-gijidomae
aoyama-itchome
kita-senju
nagatacho
akasaka-mitsuke
shinjuku-sanchome
kasumigaseki
iidabashi
ikebukuro
hibiya
yurakucho
ginza
otemachi
shibuya