I put in 112 hours into Fire Emblem Awakening, but that's only because I did all the DLC and side missions

After that there is XenoBlade - 63 hours (some side quests), Lost Odyssey - 62 hours (all DLC and side quests), and TES IV - Oblivion - 68 hours (All achievements and main side quests)

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Also if we're looking into the most time put in, I beat Super Mario RPG about 4 times now, so ~ 120 hours. Also the original Pokemon Blue/Red - 120 hours over 4 runs.

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However all those games were fun and the time blew by. Working on Front Mission 3 now, 25 hours into a probably 40 hour game, but it's dragging on because the gameplay is crap compared to Front Mission 1 & 4.

Disgaea DS. I already had a nice save on ps2 (about 230 hours), i ended up with about 350 hours on DS.

I'm not a completist, so will judge them based on my first playthrough, which can include extras but mainly what I'm comfortable doing to level up to beat the main boss.

FF12 was 80hrs or so but some of this was redundent, I spent the first 25 or more leveling all 6 characters before I realised that is not the way to do it.

FF13 was weirdly long too 70 I think. Too long. Only ever played it through once.

over 333 hours in Pokemon Silver, but that obviously included doing lots of extra stuff like collecting nearly all Pokemon (had 3 left).

Just the main game: Skyrim with 120 hours. Haven't done Dragonborn yet and thus not gathered all the achievements.
Still plenty of side quests left to do.

Longest play time: Final Fantasy XII
Longest story: Xenogears

Dark Souls w/ more than 300 hours in it.

FFXII and Xenoblade are both pretty long games; but Pokemon Emerald is probably the longest combined playtime.

Radiant Dawn has over 1,000 hours on the books though with all playthroughs combined.

The longest JRPG I played without sidequests is probably Persona 4 with 72 hours.

As for the longest JRPG with sidequests... Tales of Graces! I got the platinum trophy in that game! Tooke me more than 150 hours.

My first thought was 'Fire Emblem: The Sacred Stones', played that for about 110 hours.

Then I thought a little longer and was like: Nope, it's Pokemon Diamond, with close to 700 hours.

Xenoblade Chronicles and Xenosaga episode I both have over 100 hours put into them.