Metroid Prime - Phazon Mines
Seriously? Fighting through dark caves, legions of elite pirates and research rooms and security centers was amazing, with the Omega Pirate being the cherry on top. Granted the first time I played through that game I was scared shitless because I was young and it was a pain in the ass because I only had eight energy tanks when I first played it. But try playing the Spider Guardian in Echoes with four, because when you’re that young you suck at item collecting and exploration.
Stalker: Clear Sky - The part when you leave the swamps and there is an army checkpoint with a mounted machine gun :fffuuu::fffuuu: . the MG shoots through trees and bushes with perfect accuarcy not to mention if you stay too long in one place you get grenade-spammed by advancing soldiers :fffuuu:
Mafia - The impossible freeride-extreme mission where you need to follow a plane on a car through the city, if you fall just a little behind, BOOM you die :’(
Deus ex - The Hong-kong district, dunno I always found that part of the game dull, especially the mapping, HL has better looking maps and it’s 2 years older. The only fun place in the level is when you brake in some chicks penthouse and find a secret entrance to an MJ12 base in a toilet 
Half-life - The part in Xen where there are islands with tall spires. Lots of jumping and lots of those flying brains.
Homeworld 2 - Second level (or was it third), defend the shipyard :fffuuu::fffuuu:
I loved the Hong Kong levels of Deus Ex. They were some of the most fun in the game…
You may be happy to know that most of us devs agree.
At that time I was just taken with how cool Xen looked to care.
The final boss of MegaMan X3, I died hundreds of times and had a sore thumb by the time I beat him, I got really lucky though. Oh, and the final boss of Megaman X4, I haven’t beaten the bastard until today… If you think I’m lying just look them up on YouTube!