Not that it wouldn't work great if everyone had used transparent .pngs to begin with, but there are now a huge number of images now that look disconcertingly off with their different colored backgrounds.
Personally, I would recommend just changing the color back to what it was previously as it would save people from all the work and grief needed to fix all their images. But it's your site, so its your call though Wes. Luckily I've been using transparent .png's for all my images from the start so it's not an issue for me.
Otherwise here's a list of just the Geshrinari Shipyards article images that I've found lack the right colored background and now look strange. Nash seemed to have used transparent .pngs for at least some of the articles, but having some transparent and some solid backgrounds also makes it appear a little odd.
geshrinari:ge_c1:ge_c1_weapon_top.png
geshrinari:ge_c1:ge_c1_bottom.png
geshrinari:ge_c1
okami_top.png
geshrinari:ge_c1
okami_bottom.png
geshrinari:henkei-class_starship:ge-y1-5a_patrol_above.png
geshrinari:henkei-class_starship:ge-y1-5a_patrol_top.png
geshrinari:henkei-class_starship:ge-y1-5a_patrol_side.png
geshrinari:henkei-class_starship:henkei_above.png
geshrinari:henkei-class_starship:henkei_1.png
geshrinari:henkei-class_starship:henkei_2.png
geshrinari:henkei-class_starship:henkei_bottom.png
geshrinari:henkei-class_starship:henkei_top.png
geshrinari:henkei-class_starship:henkei_port.png
geshrinari:henkei-class_starship:henkei_turrets.png
geshrinari:henkei-class_starship:ge-y1-m3100.png
geshrinari:henkei-class_starship:ge-y1-m3101.png
geshrinari:henkei-class_starship:ge-y1-m3102.png
geshrinari:henkei-class_starship:ge-y1-m3102s.png
geshrinari:henkei-class_starship:ge-y1-m3103.png
geshrinari:henkei-class_starship:ge-y1-m3103s.png
geshrinari:henkei-class_starship:ge-y1-2a_cargo_above.png
geshrinari:henkei-class_starship:ge-y1-2a_cargo_top.png
geshrinari:henkei-class_starship:ge-y1-2a_cargo_side.png
geshrinari:henkei-class_starship:ge-y1-3a_pax_above.png
geshrinari:henkei-class_starship:ge-y1-3a_pax_top.png
geshrinari:henkei-class_starship:ge-y1-3a_pax_side.png
geshrinari:henkei-class_starship:ge-y1-4a_mine_above.png
geshrinari:henkei-class_starship:ge-y1-4a_mine_side.png
geshrinari:henkei-class_starship:ge-y1-4a_mine_top.png
geshrinari:henkei-class_starship:ge-y1-5a_patrol_above.png
geshrinari:henkei-class_starship:ge-y1-5a_patrol_top.png
geshrinari:henkei-class_starship:ge-y1-5a_patrol_side.png
starship:light_freighter_stock_.png
starship:red_nepleslian_light_freighter.png
starship
rostitute.png
starship:superstition.png
starship:thunderbolt.png
starship:cargo_runner.png
geshrinari:ge_l4:sessou_1a.png
geshrinari:ge_l4:sessou_1b.png
geshrinari:ge_l4:sessou_starboard.png
geshrinari:ge_l4:sessou_bottom.png
geshrinari:ge_l4:sessou_aft.png
geshrinari:equipment:ge-t8-e3103.png
geshrinari:equipment:ge_v1_w3300.png
geshrinari:equipment:ge_v1_w3301.png
geshrinari:amatsu-class_spaceport:amatsu_spaceport.png
geshrinari:amatsu-class_spaceport:habitat.png
geshrinari:amatsu-class_spaceport:amatsu_sections.png
geshrinari:amatsu-class_spaceport:ge-h2-m3300.png
geshrinari:equipment:senkun_computer.png
geshrinari:sanza-class_shipyard:sanza_class.png
geshrinari:sanza-class_shipyard:sanza_secured.png
geshrinari:sanza-class_shipyard:sanza_core.png
geshrinari:ge_z1:ge_z1_series.png
geshrinari:ge_z1:ge_z1_side.png
geshrinari:ge_z1:ge_z1_top.png
geshrinari:ge_d1:ge_d1_specter.png
geshrinari:ge_d1:ge_d1_weapon.png
geshrinari:suribashi_class:enkan.png