What games went beyond being merely entertaining, actually inspiring you to think about, interpret and reseach it's messages and meanings? What have been the most thought povoking games you have played?

For me it was Metal Gear Solid 2: SoL, XenoGears, Killer7 and Planescape: Torment. No other games have really inspired me to think deeply beyond face value.

Bioshock would probably be the most though provoking game of all time

No game has ever made me think in the way you describe, some games have made me think in a way such as 'whats the best strategy for this boss, whats the best route here' etc.

Conker's Bad Fur Day made me re-evaluate my stance on how well satire could be executed in playable form. Is that thought provoking enough?

metal gear solid 2.

since ive played that last week, i picture myself robbing stores at night with my friend andiry. LOL

anyways, also call of duty 4. i tactually got me thinking about joining the canadian army when i grow up. but it would just be peacekeeping missions so nah.

also bus simulator 2008. it got me thinking of becoming a transit driver if i Phail at school

Super Mario Bros.

Think about it, it totally changed the way we think about mushrooms and plumbers.

Mass Effect. I've spent many hours pondering the logistics of getting intimate with a Quarian.

Definitely FF7

Super Mario Bros. taught me that nothing is ever as it seems. A pipe can either have a monster in it or warp me to a distant land. If I jump in the air I might hit an invisible brick and break my skull. Question marks may hold coins, mushrooms, or giant beanstalks into the heavens.

Planescape: Torment, no other game comes close to it. Best videogame story of all time too.

There are also worthy mentions of Deus Ex and the Fallout series. Both of them have struck my mind several times.

Not even close.