Tomb Raider (1996) - Palace Midas
A massive, expansive level that is great fun to play through

Tomb Raider II - Opera House, The Deck
Opera House was like delving into the heart of enemy territory, and is a fantastic setting, whereas The Deck is much like Palace Midas above. I look forward to these levels on my annual TR2 run.

Paper Mario: The Thousand Year Door - Chapter 3 (Glitzville)
Someone already mentioned this. Incredible chapter that had me gripped the first time I played it. I was up until the early hours completing it as I had to know what was going on!

Super Mario 64 - Lethal Lava Land
Purely for the shell surfing.

The Legend of Zelda: Twilight Princess - Snowpeak Ruins
Someone else mentioned a Zelda dungeon, so I will too. I liked the atmosphere to this one, gradually exploring the Yeti's home.

Sonic the Hedgehog (Master System) - Jungle Act 1
Always the highlight when I play. I particularly enjoy the jovial music.

Super Mario Galaxy - Beach Bowl Galaxy
Bright, vibrant and fun.

Banjo Kazooie - Treasure Trove Cove
See Mario Galaxy above.

Super Mario Odyssey - Luncheon Kingdom
Early days with this game yet, but this level had me absolutely hooked.

Goldeneye - Surface
Running round killing enemies in the snow with all weapons and infinite ammo never gets old.

I just played the New Donk City 2D level of Mario Odyssey and I think it has become one of my favorite levels. It is very reminiscent of the good old days, but it is also flashy and also the music is a nice touch!

Every single level of Donkey Kong Gameboy.

Mario 64 - Tiny Huge Island

Donkey Kong Tropical Freeze - Windmill Hills

Mario 3D World - Great Goal Pole

Ocarina of Time - Spirit Temple

Terminal - Modern Warfare 2

Valhalla - Halo 3

Dust II - Counter Strike

Turok 2 - Port of Adia

Goldeneye N64 - Caverns

Bafford's Manor in Thief The Dark Project.

New York in Deus Ex.

A New Life and A Dance With The Devil in Hitman Blood Money.

Happiness and Metro City in SSX3.

Noork's Elbow in Unreal.

First area in Full Throttle.

Sumo Sky Palace in Shadow Warrior.

Na mean?

Super Mario Bros - Stage 1-1
Super Mario Sunhine - Ricco Harbor
Super Metroid - Lower Brinstar
Metroid Prime 3 - Pirate Homeworld
Metroid Other M - Sector 2
Zelda Breath of the Wild - Hyrule Castle
Zelda A Link to the Past - Desert Palace
Zelda Majoras Mask - The Moon
Zelda Twilight Princess - Snowpeak Ruins
Resident Evil 2 - Police Station
Resident Evil 4 - Pueblo after sunset (Chapter 2, I think)
Terranigma - Sylvain Castle
Secret of Mana - Ice Country
Donkey Kong Country Tropical Freeze - 5-6 Frosty Fruits
Deus Ex Human Revolution - Tai Yong Medical
Final Fantasy I - Sky Fortress
Final Fantasy II - Dreadnought
Final Fantasy III - Living Woods
Final Fantasy IV - The Moon
Final Fantasy V - Great Forest of Moore
Final Fantasy VI - Phantom Train
Final Fantasy VII - The Slums of Midgar
Final Fantasy VIII - Balamb Garden
Final Fantasy IX - Alexandria
Final Fantasy XII - Dalmasca Westersand
Final Fantasy XIII - Eden
Mega Man X - Armored Armadillo Stage
Mega Man 4 - Dust Man Stage
Contra III - Stage 3
Super Castlevania - Stage 3
Yoshi's Wooly World - 5-6 Up Shuttlethread Pass
Sin & Punishment Star Successor - Undersea Tunnel
Star Fox 64 - Zoness
Star Fox Zero - Sector Omega
Xenoblade Chronicles - Eryth Sea (but actually every region is beautiful)
Xenoblade Chronicles X - Noctilum (again, every region is beautiful)
Jet Force Gemini - Rith Essa
Pikmin 3 - Garden of Hope
Bayonetta 2 - Chapter XIV The Witch Hunts
Sonic the Hedgehog - Star Light Zone
Sonic the Hedgehog 2 - Mystic Cave Zone