Gordon Freeman's final smash would be Super Gravity Gun. His special attack would cease to be the normal Gravity Gun that can pluck items and projectiles and launch them, but would be able to grab and launch players as well for a short period of time.
Alyx's final smash would be DAWG POUND. Dawg would come out and pound folks.
Glados' final smash would be FAST ACTING NEUROTOXIN. It would cause significant damage to anyone inside the cloud in 5 seconds instead of 5 minutes.
Chell's final smash would be Terminal Velocity. Close range attack that traps the victim in a top-down infinite portal loop. After terminal velocity has been reached Chell moves the bottom portal for an insta-kill slam.
The TF2 Defense Trio's final smash would have Level 3 Sentry, Pipebomb spam, and a bonus sandvich that heals user for 25% as the mayhem ensues.
The TF2 Offensive Trio's final smash would have Crockets raining down and Crit-fire surrounding the point where the final smash was initiated, the user would drink a Bonk! energy drink and be invincible during the final smash and a little bit after the weapons stop.
The TF2 Support Trio's final smash would offer an instant kill, the player would get a targeting reticule, whoever he/she manages to hit gets backstabbed and headshot (600% damage if walls prevent insta-kill) at the same time. The player would be healed for 100% by an OKTOBERFEST drink upon successful final smashing.
The Survivor's final smash would be Boomer Bile. Anyone hit by the splash of the bile-containing canister will be rushed unmerciful by the horde.