The way I see it, it's impossible to judge a movie without adding some subjectivity. At the same time, I find it weird when self-proclaimed movie buffs will admit that some of their favorites are "objectively bad". In my opinion, a favorite should be a movie you find objectively good and have a particular soft-spot for.
For instance: I find The Good, the Bad and the Ugly to be objectively good and it's also one of my personal favorites. But I wouldn't claim that it's better than The Godfather, even though the latter isn't among my favorites at all. I enjoy watching Rocky IV for nostalgic reasons, but I also think that it's a terrible movie. Because of this, I wouldn't count it as one of my favorites. I get warm and fuzzy inside when I turn it on, but I also cringe while watching it. I believe the right term for this is "guilty pleasure".
But back to your original question. Here are some of my "newer" favorites(I have excluded my favorite movies made before 1990):
In The Mood For Love
Kikujiro
Spirited Away
Millennium Actress
Paprika
The Shawshank Redemption
The Fellowship of the Ring
Oldboy
Lost in Translation
Perfect Blue
Office Space
Reservoir Dogs
Django Unchained