Never played MGS3.  Only played MSG4 and the original NES game.  I know it has a convoluted story, but I was guessing your clue was referring to Big Boss.  Guess I stumbled into the correct answer anyway.

7 Final Fantasy 4
6 IIRC, that is either Super Mario World or Donkey Kong Country depending on whether you count a pack-in as the best selling game.

2 is correct!  3 and 4 are not.  4 is actually a less obscure game than you guessed.  3 on the other hand, people have trouble guessing it every year.

Correct on both!

Guessed by The_Liquid_Laser

Or wait, maybe this is the game that wins the crown of my most played ever. Yeah, probably this one. The funny thing is, even though I played this game so much, I never even touched the scenarios. I always made my own sandbox level with the included editor, and then played that map for a couple hundred in-game years. An in-game year takes about an hour, I think it depends on some computer specific factors in how much time it is exactly, but anyway you can imagine how long I took on a park perfecting it. And I had a bunch, next to another bunch that I worked on for a shorter amount of time. I didn't really like stuffing my game with a lot of user created scenery items, so most parks I made I did with vanilla assets. I mastered it, the screenshot is mine, and that's the strength of this game. Its core gameplay is so simple yet effective that everyone can pick it up and play, but if you try you can build anything you want.

So after four Construction & Management games in the last six entries in the list, RollerCoaster Tycoon 2 is the best of such games ever made. Top 5 inbound. We're almost there.

#5: This game actually introduced a lot of this series' mainstays, like a wise guide character, but never really gets the credit.

#11 BlazBlue Calamity Trigger

Every character in this game has a unique ability that is activated by pushing the special move button. The special move button works similair to a kick or punch button. Pushing any one of four directions plus the special move button will result in one of four different attacks. Sometimes more if there are air variants of moves. This opens the game up to a lot of creativity not seen in other fighting games. This is because in other fighting games you would need a unique input like quarter circle plus punch for each special move. But there are only so many of these inputs you can put into a game before special moves start firing off unintentionally. But on top of having a special move button there's also a bunch of these inputs as well. This let's the game have about double the special moves per character as any other fighting game. Also every fighter has their own unique power to use. The grappler uses magnets to pull enemies closer. The swordsman stocks power and then slashes away with devastating cuts. The catgirl bounces around the screen like a madman. The combos are easy to pull off, but the game is still highly technical, thanks to a shielding system. I never quite felt like the combos were so oppressive in this game that you were dead after three good combos. The animations are fantastic. Just look up Rachel's animations on Youtube. IMO this is the best of the Blazblue series, and other games in this series suffer from feature creep. In subsequent titles combos become too hard to pull off, the roster is too big, and the animations suffer. The sequels took a lot of good characters and completely changed how they work, while adding in other characters that are just bad copies of already existing characters. 

#4: Final Fantasy Tactics

#3: Freedom Force

The way both Rescue Team and Explorers got trashed in reviews are the reason I don't read reviews. I was only 9 at the time but it was painfully obvious that they either hadn't played the games (the Gamespot reviewer even admitted that they didn't get 10 hours into a 50+ hour game!) or just didn't want anything that wasn't mainline Pokemon. You should definitely check Rescue Team, Explorers and Conquest out - the Pokemon spinoffs are actually better than the mainline games IMHO.

#10 Final Fantasy VI 

Many people credit Final Fantasy VII as the best game in the series, but FFVI does almost everything both before, and better than FFVII. The active time battle system that adds tension to turn based combat was there first. Epic cutscenes like the opera scene were done with excellent spritework, that holds up better than FFVII's CGI. There were over ten unique playable characters each with their own story arcs and questlines. The esper leveling system allowed you to give any character whatever moves or stats you wanted. Most games threaten to end the world, if you don't defeat the bad guys, but FFVI actually does end the world halfway through the game. Oh and did I mention you can suplex a ghost train in this game? 

#9 Chrono Trigger

One of the most important things, gave developers need to learn is that AGLs in games are bad. What are AGLs? Artificial Game Lengtheners (full credit to Dunkey for the acronym), are the parts of a game that are tedious and time consuming simply for the sake of lengthening a game. Oftentimes a game will be fun, but will only take ten to twenty hours to beat. For some reason development studios see that as unacceptable, so they use AGLs to spread the fun content out like too little butter over so much toast. I believe that the JRPG genre is one of the greatest things ever invented in this medium, but I also admit that most overstay their welcome by about fifty hours. The genius in Chrono Trigger is that it removes most of the standard AGLs from the genre leaving pure fun in it's wake. Random battles are gone. Turn based combat uses the speedy ATB system from FFVI. Enemies are placed and spaced out so that you fight them only enough times to hold your interest and no more. Chrono Trigger only takes about twenty to twentyfive hours to beat, but it's a breakneck rollercoaster ride of fun from start to finish. This game has excellent character designs from Dragonball's Akira Toriyama, and a perfect soundtrack by Yasunori Mitsuda. There's a really fun and interesting combo system built into the game, that feels natural. You can combine different attacks like a flame attack, and a sword attack to get a flaming sword attack (See the cover?). Multiple endings and a New Game + mode mean anybody that loves JRPGs should be in for a good 50 hours of completionist playtime. The original SNES cart still commands $80 or more despite DS and PS1 remakes existing. This is the JRPG that transcends hatred of JRPGs. Even if you absolutely hate the genre, you owe it to yourself to play this one. Yeah, it is that good.

Well, I fell way behind. Instead of trying to catch up, I'll just try to finish with my top 6

6. This game features a song with lyrics in Esperanto.
5. Often described as an offline MMORPG, when it released
4. I like this game beacause I'm a puppet