Some of these comics were translated just for fun by an anon in /mmg/, the megaman general on 4chan, and typeset by another anon. Most everything else has been gathered over the years across the internet. They're all roughly 10 (or so) page comic shorts.

SplashFlash Comics (English)
shademan_comic.cbr (English)

Rockman X4 manga (Japanese)
rockman_x5_-_the_beginning.cbr (English)
white_breeze.cbr (English)
mr._zero.cbr (English)
axl_and_red_comic.cbr (English)
axl_and_x.cbr (English)
axl_bullies_vile_comic.cbr (English)
vile_and_vavako_comic_traducao.cbr (English)
vile_the_third_wheel_comic.cbr (English)
x_and_rock.cbr (Korean)
zero-format.cbr (Japanese)
mega_man_card_baka.cbr (English cards)
rockman_x_mega_mission_jumbo_carddass.cbr
Rockman X Gigamission (English/Japanese)

Rockman Zero 3 Modification Cards (Japanese)
zero_4_short.cbr (Japanese) Fancomic of the Zero 4 ending.
megaman_zero_date_night_by_eriance.cbr (English)
freesia.cbr (English)

Nothing here yet :(

Nothing here yet :(

Nothing here yet :(

Nothing here yet :(

Maverick Hunter: Special Forces (Because I'm a dork and I can)
Pocket Gamer