Reversed Kanji with the same pronunciation

事故 ji ko - (traffic) accident
故事 ko ji - tradition, historical fact  [submitted by Eduardo]

慣習 kan shuu - usual (historical) custom
習慣 shuu kan - custom, habit, manners

名著 mei cho - famous book, masterpiece
著名 cho mei - well-known

魚雷 gyo rai Torpedo
雷魚 rai gyo A type of fish - snakehead mullet (whatever that is...)

進行 shin kou progress, advance
行進 kou shin march, parade

和平 wa hei peace
平和 hei wa peace

画面 ga men terminal screen, scene, picture, the field (in TV), photo
面画 men ga surface-drawing

社会 sha kai society
会社 kai sha a business

決議 ketsu gi a resolution, resolve
議決 gi ketsu

議会 gi kai an assembly
会議 kai gi a meeting

議論 gi ron an argument; a discussion
論議 ron gi discussion; to discuss or talk about

楽器 gakki - a musical instrument
器楽 ki gaku - instrumental music

光栄 kou ei - honor, glory, privilege
栄光 ei kou - glory

海外 kai gai foreign countries
外海 gai kai open ocean

数人 suu nin - Several People
人数 nin zuu Number of people

材木 zai moku - wood, lumber, timber
木材 moku zai - lumber

実現 jitsu gen - realization (of a dream)
現実 gen jitsu - a reality, actual, real
 

日本 nihon Japan
本日 hon jitsu Today

家出 ie de  running away from home, leaving home
出家 shukke entering the priesthood, priest, monk

力学 rikigaku mechanics, dynamics
学力 gaku ryoku scholarship, knowledge, literary ability

男優 dan yuu actor
優男 yasa otoko man of gentle manners

根性 kon jyou will-power (vs), guts, temper, nature, spirit
性根 shou ne character, nature

様子 you su aspect, state, appearance
お子様 o ko sama child (polite)

凸凹 dekoboko - rough; uneven
凹凸 ou totsu - unevenness; uneven

敬愛 kei ai - respect & affection
愛敬 ai kyou - love & respect

口出し kuchi dashi - meddling, interference
出口 de guchi - exit

切腹 seppuku - commiting suicide by cutting the stomach
腹切り harakiri - same as above