Though Square Enix is a shell of how good they used to be, they still hold most of my fave titles.
I lived during the Squaresoft AND Enix/Tri-Ace ages, two separate entities, and as such will talk about titles for both companies before/after they merged.
In order of my particular faves from both companies.
1. Final Fantasy VII: Needs no introduction. Whether you played it or not, you KNOW this game. I have a special attachment to this game. No, it's not my first FF. I played FFVI (FFIII in the US) before it, many years before. But everythinhg about FFVII touched me, and resonated with me for many years. The characters, the world/setting, the music, etc. It was the complete package. An epic fantasy game that I visited and beat over and over again. To this day, it still has my very favorite video game characters, particularly Tifa, Yuffie, Cloud, Vincent, Zack. It remains my favorite game/setting of all time. I still literally dream about this world more than anything else.
I am absolutely stoked about the FFVII Remake, and I'm extremely hopeful of it.
2. Chrono Trigger: This was actually my very first RPG that I played fully. Before I got into RPGs, I played Capcom's Breath of Fire first, but didn't like it at the time. RPGs were too stiff for me, I thought. So I gave up BoF and tried Chrono Trigger. It literally blew my mind, and made me a rabid RPG fan, enough to go back to BoF and love it. Chrono Trigger is arguably the greatest game of all time. A masterpiece.
3. Star Ocean: The Second Story (now called Second Evolution): SO2 was a hit that came out of nowhere for me. I rented this game, and immediately fell in love with the massive world, characters, battle system, private actions, etc. It felt like a good alternative to something out of Final Fantasy, yet different enough to enjoy, particularly if you liked a faster paced, action battle system. I literally rented and beat this game like 8 times, lol. It's a fantastic game to revisit over and over again.
4. Valkyrie Profile (now known as VP: Lenneth): The rich, character driven game, where you are a god harvesting souls to help you in battle. The premise blew me away. The countless characters, awesome music, special attack animations were all memorable, and is still amazing today.
3. Xenogears: Came out around the same time as FFVII, and I couldn't believe just how much Square had game epics dialed in. Xenogears was controversial, massive, incredibly complex, and fun to play. It was flawed, with a rushed second disc, but it didn't matter. This is a cult classic for a reason. A game that made you question life. The plot twists, the battle systems (there were basically two, not counting the mini game battles which was also very good). It was an amazing title, in the golden age for Square.
4. Final Fantasy VI: My second Square game I ever played after Chrono Trigger, in a time I didn't really know much about RPGs, let alone what FF was. I remember playing it and thinking to myself (wow, this game is amazing, how come I never heard of it)? Of course, I was a young teenager, lol. FFVI may not be my FAVE game of all time, but I have to say, it is what I and many consider to be Square's BEST Final Fantasy. I honestly can't argue with that. I may prefer FFVII, but I do feel FFVI is overall the better game. It was massive, with many characters, many plotlines, and depth, which still holds up today. This is coming from a 16bit game. So much, came from something so little. If you're a fan of RPGs and haven't played FFVI, stop what you're doing, and play it. It is a masterpiece.
5. Super Mario RPG: Legend of the Seven Stars: Yes, this was a Nintendo/Squaresoft joint venture, and it paid off amazingly. This is EASILY my favorite Nintendo title of all time. I played this game so many times, I lost count. It was actually a bit short for an RPG (back then I would take a week to beat an RPG, this one took me just over a day or two), but it was so fun, so active, and so charming. Many fond memories. NINTENDO, WHERE IS GENO AND MALLOW?
6. Final Fantasy IV (particularly, the PSP Remake): FFIV is a classic. Those who played it know the story is a simple affair with incredibly memorable charcter characters, such as Cecil the Dark Knight turned Paladin, and Kain, the best friend, a Dragoon in love with Cecil's woman. A complete cast of memorable characters and rich world/story despite it being a bit more basic instructure than FFVI. The PSP remake is thje best iteration, which kept the classic feel, with overhauled sprites. It is the best version of the game, IMHO. The DS 3D version was good, but it didn't have the same feel as the classic, which the PSP version kept.
I'm sure I'm missing many, but I'll stop here. Notice how my faves are all PS1/SNES era games. That was when S-E was in its prime.
Of course, there are newer stuff I loved. The 2013 Tomb Raider was amazing. I can't wait for Rise of the Tomb Raider to hit PC next month. I don't have an XB1, so I've been waiting for PC or PS4 release.