Here's a list from Breakpoint to get you started that includes To Kill a Mockingbird, It's a Wonderful Life, The Little Mermaid, Aladdin, Frequency, October Sky, Minority Report, Spider-Man, Road to Perdition, We Were Soldiers, Life Is Beautiful, Finding Nemo and a few others.

That can't be all?

What, no Magnolia?

The Bicycle Thief would be another I would add to the list.

Haven't read the Breakpoint link yet, but someone played a clip from Frequency at an event I spoke at last weekend, and I remember Charles Colson sang that film's praises for the way it showed how a man needed a father in his life. (I'd love to see that film again, too.)

I'd include The Twilight Samurai.

I may not have cared for the film all that much - and it's not a film that deals just with fatherhood - but I loved Donald Sutherland's performance in Ordinary People, and would add him to the list.

What, the dad from C.H.O.M.P.S. wasn't good enough to make the list?!?!

Where is Judge Hardy? (Yes, I'm old - but not that old)

Hmmm, just realized no one had mentioned The Return yet ...

I would include:

Hotel Rwanda
I am Sam
Koyla (adopted father)
Marvin's Room
Radio
Shine
A Walk to Remember

Denny

I've been asked to recommend Movies For Father's Day.

What are some more great films about fathers?

The Jazz Singer (I'm thinking of the remake with Neil Diamond since I haven't seen the Jolson verison)
In America
The Godfather (interesting father/son relationships)
Star Wars Episode V: The Empire Strikes Back "I am your father."
Get on the Bus
Indiana Jones and the Last Crusade
To Kill a Mockingbird

The Shining
There Will Be Blood
Around The Bend (three generations of fathers)
My Fair Lady
Mary Poppins

Not sure how many of these could be classed as great - more popular than great - but they do have an interesting father-child relationships, at different stages of that relationship

Road to Perdition
Sleepless in Seattle
Father of the Bride
My Girl
Cape Fear
Thank you for Smoking
My Son the Fanatic
Les Mis

How Green Was My Valley
Dead Poets Society
A River Runs Through It
Hamlet
Return of the Jedi

War of the Worlds
Signs
Kramer vs. Kramer
Lion King
Finding Nemo
About Schmidt
Big Fish
Austin Powers In Goldmember
Three Men and a Baby
In the Name of the Father
Life is Beautiful
Meet the Parents
Father of the Bride
The Brady Bunch Movie
Billy Elliot
Matchstick Men
The Courtship of Eddie's Father
Slums of Beverly Hills
The Savages

If you're looking for one that actually has something positive to say about fathers on Father's Day, try The Flamingo Kid. Charming, gentle little coming-of-age-and-wisdom movie.

From the original list, October Sky and Mockingbird are good choices. Also The Man in the Moon, from the same director as Mockingbird.

On the depressing side, one that no has yet mentioned is All My Sons, from the Arthur Miller play.

Nor Death of a Salesman which has numerous TV incarnations and a 1951 film version starring Fredric March.