(not a part of my best of's but has a lot of cool lists)

The small tops list of films I have seen:

Blade Runner

Boys Don't Cry

Donnie Darko

Wit

But I'm a Cheerleader

Lost in Translation

Lost and Delirious

La Femme Nikita (1990)  (shockingly violent)

My Summer of Love
The Dreamers
Paprika

Niagara, Niagara

The chronological tops list of fiction films I've seen includes:

Before High School:
Shawshank Redemption
The Godfather
The Godfather Part II
Leon the Professional

Goodfellas
The Game
Golden Child (fun action-comedy)

(I remember watching a lot of violent movies as a young boy; which I now think is sad)

High School: 
Contact
As Good as it Gets (Mental Health)
Girl Interrupted (Mental Health)
A Streetcar Named Desire
Trainspotting
Fight Club (thrilly-violent)
Go
Gross Point Blank
Gattaca
Enemy at the Gates
A Beautiful Mind                                                                  
Eternal Sunshine of the Spotless Mind                                                      
Chicago
Something the Lord Has Made
Iron Jawed Angels
Can't Hardly Wait
Memento
Angels in America

Undergrad:
Million Dollar Baby
Training Day
Taxi Driver (natural and violent all at once)
El Labirinto del Fauno
El Orfanato
L'enfant (slow, real, and moving)
Looking for Bobby Fisher

El Mar Adentro
Blue
Goodwill Hunting

You Kill Me
Unbearable Lightness Of Being
Closer
Science of Sleep
Starting Out in the Evening

Vera Drake

Layer Cake (a little on the violent side)
Walk the Line
Battle Royale
12 Angry MenLittle Miss Sunshine
Before the Devil Knows Your Dead (jarringly and domestically violent)

Post Undergrad:
Gandhi
Choke
8 1/2
Three Times
The World
Annie Hall
Mrs. Henderson Presents
All The Kings Men
Katyn
Say Anything
High Fidelity
Niagara, Niagara (Mental Health)
BRD-Trilogie: The Marriage of Maria Braun
Lola
Veronika Voss
Kanal
Thirteen Candles
Breakfast Club
Hugo
La Estrada
Nue propriété
Jack Goes Boating
Seven Samurai
Arigatô-san
Orpheus
A Dangerous Method (Mental Health)
Loves of a Blonde
Ugetsu
Drive (really pushing the realistic violence)
Beasts of the Southern Wild
Shame
Spirited Away
The Master

Weekend (LGBT)

Like Someone In Love
Bez Wstydu
Hemel
Fabro de Rato
Paperboy                            
Lincoln
Holy Motors
Dogville
El Premio
Soog
Bande à part
Metropolis
La Bohème
집으로 – Jibeuro
Princess Mononoke
Castle In the Sky
Beyond the Hills
Hikaru no GO (TV)
The Sapphires
Elles
Fullmetal Alchemist Brotherhood (TV)
Fruitvale Station
Tokyo Godfathers
Certified Copy