Five?! Only five? My top 5 list varies depending on my moods cause I tend to not have favorite games in any particular order...
Legend of Zelda: Ocarina of Time 3D -
Grezzo essentially hijacked my mind, saw what my nostalgic self thought of OoT after 12 years, and made it into a game that usurps the original. As a kid I fondly remembered beautiful night skies and colorful places full of small details, as well as charming hiccups like sharp polygons and flat fire because of the N64's graphical qualities. This game has all of that, just as my childhood self remembers it. I doubt I'll ever see another remake that perfectly balances nostalgia with modernity. It's no mean feat, achieving that balance, and I completely understand how Square is afraid to try it for FFVII.
Yakuza 2 -
Great story, great world, great characters, great sidequests, great battle system. It captures the "nightlife" feeling perfectly, and it's one of my favorite atmospheres in gaming. I have a slight fascination with the "ninkyou eiga" type of yakuza stories, and as such I adore this series.
Elder Scrolls 3: Morrowind -
To date the most interesting lore I've ever seen in a game. The combat system blows, but the feeling of "survival" is unrivaled in my mind. It is tough to explore at first, but if you stick with it, you'll become more comfortable and powerful.
Deus Ex: Human Revolution -
Got me into cyberpunk, which is another of my favorite aesthetics now. The contrast of high technology for the rich and the shit-dregs of the poor, and navigating between both through wonderful art direction and detailed settings just completely drew me in. I love the way it balances non-linear sidequesting and the guided campaign. And I love vents. I never look at them the same way again after that game, lol.
Final Fantasy XII -
My favorite Final Fantasy game, bar none. No daddy issues, no chosen ones, no teenage-quality writing and drama, no egregious belts and zippers, no schizophrenic art direction, no crushing linearity, no random encounters, and no anime-quality English dubbing. Sadly, no Nobuo Uematsu either, but that's a small price to pay.
Here is what it does have: The most mature writing in the series (at worst it's charmingly ostentatious) subtly expressive characters that are far from flat in spite of being chiefly driven by the plot, the most open, alive and cohesive FF world I've ever played in (visually, culturally and historically), an intriguing plot between warring nations, a fantastic battle system that makes the traditional grind incredibly bearable, and so many subverted FF tropes. I know the OP said no negative comments but...it makes me sick to my ass that people lump this into the "decline of square." The same fans who ***** about the usual FF suspects got a game that subverted all of that, and complained. Then they got it all back in FFXIII, and they still aren't happy. Sad.