Lighting... I Don't get it!
Using different textures may help too, some have different volumes of reflectivity than others. Observation rooms are also a must, and are best put at high places. This way they can illuminate the usually dark ceilings and high walls. Light panels are best placed on low walls and ceilings. Looking from the pictures you provided, you may want to try the warm panel instances around the door, but the cool panel instances in the actual room. Valve usually uses the warm panel instances to draw the player's attention to certain game-play elements. You can find examples of this during the Single-player and Coop Campaigns.
Good Luck!
To make the glass lights lighter, just change the white light texture to a higher number in the face edit from .25 to 8
For me I like to add lights near entities e.g:
prop_tractor_beain, in the middle of the base, a light_spot with a blue light and change the color with an input if it reverses
Floor buttons, a small red light in the middle of the button
Doors, add a grey light_spot pointing to it
Gel droppers and cube droppers, add a grey light for the cube droppers, and use orange, blue, or white for gel droppers.
grey lights on the laser emitters
Light bridges, add a sky blue light,
Faith plates, add a grey light.
I just put a prop_static glass_light on the ceiling and a light entity under it.
My Work
[spoiler]Maps:
Revenge of the Angry Turrets
Capture the Cube [Co-op]
Capture the Cube 2 [Co-op]
TPWEGTH Sample Map
Aperture Aquatic Testing Center
Aperture Aquatic Testing Center 2
Aperture Time Testing Center
ML's Halloween Trick - 1000 downloads!
ML's Halloween Treat
ML's Combination - 1000 downloads!
ML's Jailbreak Labyrinth
ML's Tricky Teamwork [Co-op]
WIP:
"Capture the Cube 3"
Workshop Maps Link: http://steamcommunity.com/profiles/76561198008890579/myworkshopfiles/[/spoiler]
Thanks All for replying... I'll decompile some maps and take a look at what valve did. Thanks for all the tips 
