In the Famitsu magazine, it has listed the top 100 games of all time.

1. Final Fantasy X (2001)
2. Final Fantasy VII (1997)
3. Dragon Quest III (1988)
4. Dragon Quest VIII (2004)
5. Machi (1998)
6. Final Fantasy IV (1991)
7. Tactics Ogre (1995)
8. Final Fantasy III (1990)
9. Dragon Quest VII (2000)
10. Legend of Zelda: Ocarina of Time (1998)
11. Dragon Quest V (1992)
12. Far East of Eden 2 (1992)
13. Sakura Taisen (1996)
14. Dragon Quest IV (1990)
15. Final Fantasy V (1992)
16. Xenogears (1998)
17. Dragon Quest II (1987)
18. Sakura Taisen III (2002)
19. Kingdom Hearts (2002)
20. Streetfighter II (1992)
21. Super Mario Bros (1985)
22. Final Fantasy VIII (1999)
23. Toki Meki Memorial (1995)
24. Final Fantasy IX (2000)
25. Final Fantasy VI(1994)
26. Metal Gear Solid 3 (2004)
27. Valkyrie Profile (1999)
28. Chrono Trigger (1995)
29. Kingdom Hearts II (2005)
30. Dragon Quest (1986)

Seemingly, a majority of it are Square Enix games, even 7 of them being in the top 10 alone.

Check the rest of the list here: Gamed