It's a Wonderful Life (1947)
The Graduate (1967)
The Swimmer (1968)
The Last Picture Show (1971)
Save the Tiger (1973)
Network (1976)
Risky Business (1983)
The Big Chill (1983)
The Breakfast Club (1985)
Hannah and Her Sisters (1986)
Blue Velvet (1986)
Ferris Bueller's Day Off (1986)
Sex, Lies, and Videotape (1989)
Crimes and Misdemeanors (1989)
Husbands and Wives (1992)
Short Cuts (1993)
Groundhog Day (1993)
The Ice Storm (1997)
Eyes Wide Shut (1999)
Wonder Boys (2000)
Six Feet Under (HBO series, 2001-05)

Not a film, but Breaking Bad (the TV series) and season 1 of the Fargo (the TV series).
Wendy? Darling? Light, of my life!

The Apartment
I bet if this movie had been made in the 50s or 60s, Jack Lemmon could have played Lester
~ I'm a 21st century man and I don't wanna be here.

Revolutionary Road. Also directed by Sam Mendes.

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blytheoakman: Do you have any to add, 10 months after your OP?
My suggestions:
Hurlyburly (1998) also stars Kevin Spacey
The Cider House Rules (1999)
A Home at the End of the World (2004)
and Wonder Boys (2000). is one of my faves.

"Election" (1999) directed by Alexander Payne

-Garden State, I second that.
-The Wackness (2008) with Ben Kigsley is also really similar. It basically has same worldview about the friendship between an 18 y.o. boy and an older man in midlife crisis, who are smoking weed together.

it's quite some time since you opened this thread, but if you're still interested have a look at Six Feet Under. It's created by Alan Ball (the writer from American Beauty) and has a lot of similarities with American Beauty.

Monster's Ball (2001) does remind me a lot of the darker moments in this movie.

I find Office Space to be similar in the tone of the main character's transformation

Lolita

The Ice Storm (1997) definitely.
WARNING: I'M SEXY!

Ice storm. It is set in the early 70s. Its a little more heavy on the teenagers

Little Children, Pleasantville, Who's Afraid of Virginia Woolf, A Streetcar Named Desire, Far From Heaven, Blue Jasmine and another Mendes film Revolutionary Road

https://pbs.twimg.com/media/CRZrfuSVEAALhQV.jpg

A few that come to mind are The Squid and the Whale and The Royal Tenanbaums.

Lymelife
Submarine
Garden State
The Ref
City Island
Shame
Before The Devil Knows You're Dead
I don't love her.. She kicked me in the face!!

All these are very good I would add the film Seconds (1966)

These are films about midlife crisis I can think of.
Dodsworth (1936)
The Swimmer (1968)
Husbands (1970)
10 (1979)
A Serious Man (2009)

I found Donnie Darko, though much more science fiction, to be very similar in tone and message.

Ordinary People
~ I'm a 21st century man and I don't wanna be here.

I love Magnolia more than American Beauty.
I'm with you on that, pinokiyo Magnolia has aged well, while I can't say the same for American Beauty. - at least, to me, basing that on the fact that American Beauty USED to be a favorite of mine, but has faded out. It's a good performance by Kevin Spacey. Magnolia was and still is one of of my favorite films. Tom Cruise is good; EVERYONE is good in Magnolia.

Magnolia - which also came out that same year 1999. I highly recommend that one. In fact, I love Magnolia more than American Beauty.
It follows the life of people and how imperfect they are. Tom Cruise is gold in that film.

Happiness too.