The 90's was a pretty nondescript decade, and there was nothing that stands out about it, as opposed to the 80's (I can spot an 80's hairstyle a mile away) or the 70's (the early 70's being very hippy and the late 70';s being disco)

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"So I Married An Axe Murderer"
"There's Something About Mary"
"My Best Friend's Wedding"
"Four Weddings and a Funeral"
"Twister"
"Forrest Gump"
"Armaggedon"
"Pulp Fiction"
"Under Siege"
"Austin Powers: International Man of Mystery" (references that it is in the nineties, and the sequels might as well have been released in the nineties too)
"Sabrina" (a remake, but references the decade and the filmography is in that noticeable style)
"The Parent Trap" (another remake, but totally nineties)
"Beverly Hills Ninja"
"Ransom"
"Braveheart"

Anyone yet mentioned Dazed and Confused? (even though set in the 70's, it was a definitive 90's film for me).

Clueless (1995), City of Angels (1998), American Beauty (1999), Batman Forever (1995)

Cool thread. Many good suggestions.
I believe no one mentioned Baseketball yet. It's got many 90s pop culture references that are unknown to kids who were born in the 00s and beyond: Scatman, Jerry Springer, Nintendo, Unsolved Mysteries, Christian Slater & Robert Downey Jr's reputation as alcoholics, Yasmine Bleeth, etc.
You try and hurt Mozart? You're gonna get a bullet in your head courtesy of Butch Cassidy.

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Cool thread.

Before Sunrise
While You Were Sleeping
Wedding Singer
The Truman Show
Chungking Express
Amlie

I saw it. A thing that was cold and dry. It was me. - La Belle Noiseuse

Mrs. Doubtfire
Clueless
Space Jam
Sleepless in Seattle
Speed
Liar Liar
Point Break

The first Bad Boys, Scream, Clueless, 4 Weddings And A Funeral, Home Alone, Pretty Woman, Ace Ventura.

class act and house party

I miss the 90s! I think that all of my favorite 90s movies have been listed, but what about cheesy cartoons like Fern Gully?

Dirty Work
Half Baked
Speed
True Lies
Enemy of the State
Big Daddy
Suicide Kings

I don't think there's so much more nineties, funny and good like A Night at the Roxbury, and yes I would say Clueless too, but a lot of people has mention it before, so I would say that
If it's about schools and killing your professors or your professors wanting to kill you:
Teaching Mrs. Tingle - 1999
Killing Mr. Griffin - 1997
The Faculty - 1998
A cheesy film:
Can't Hardly Wait - 1998
About dramas:
Girl, Interrupted (I'm not so sure about this, but it definitly have the nineties look)
Night on Earth - 1991 - A Jim Jarmusch not so well known film that definitly have the nineties look.
Very good question, you made a very nice question that became a very cool forum.

Clueless. Speaking of which there were three actors from Clueless in this movie.

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Anyone mention Double Dragon yet?

Zohan actually

All the "Scream" movies and "I Know What You Did Last Summer."

I always thought High Fidelity had a 90s feel about it - I think it was made in 2000 though so this'd be the reason why.
"Would you say you're a fairly egregious person?"

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Don't tell mom the babysitters dead.
Buffy the vampire slayer
Elvira mistress of the dark is the coolest woman ever.
DCI Gene Hunt (UK) coolest man ever.

"My Best Friend's Wedding" starring Julia Roberts. SO '90s! The clothes, the hair, the cell phones! I love that movie.