1) Frontlin (Team Fortress mega). At the time Team Fortress maps were dominated by the capture the flag mechanic. Frontlin dared to be different by giving each team an objective to destroy inside the enemy base that could only be taken out by a demonman's demolition charge. The map also included features never seen before in such games including a helicopter that would insert players near the enemy base, mortars, jungle segments and so much more.
2) Scarabrae (Tribes). Tribes had plenty of good maps but Scarabrae is certainly the best. The map features two very large bases placed .9 km apart separated by a massive crater. In the middle of that crater was a lone control point that housed an inventory station and a missile turret. Each base hand multiple entrances and power sources and this was the map that offered the most clever defenses, especially when using the renegades mod. Of course, nothing was better than booking it to the enemy base as a spy and planting satchel charges before their engineers fortified the hell out of the generator room then blowing up the generators forcing them to spend several minutes carving away the epic defense they so painstakingly placed to prevent this very occurance.
3) DM17 (Quake 3). This is, without a doubt, the most famous map in Quake 3. The open nature of the map ensures that you will always be in line of sight by someone. Better than that the map does a better job of managing risk and reward than any map I've seen since. Want to get the railgun? You'll have to make a long jump that can be interrupted by something as simple as the machine gun. Want that mega armor? You'll have to walk across a narrow ledge over oblivion and risk a single rocket knocking you to your doom. Want that Quad damage? You have to make TWO lengthy and vulnerable jumps to get to it!
4) TFort5r (Team Fortress Mega). Probably the iconic CTF map for people playing games today. This map was largely identical to the modern 2fort people play in TF2 today with a few differences. For starters, to discourage camping outside the opposition's fort, a pair of rottweilers (where that r comes from) waited to mangle anyone who dared linger (they had absurd health and if they did damage they caused the player to slow until they received medical aid). The only other major change was simply that there was no cover over the bridge connecting the two sides making any crossing a hilarious danger. And the water route wasn't much safer thanks to the existence of toasters (a grenade item available to all classes. When thrown into the water it would kill anyone that had line of sight to it.
5) The Rock (Team Fortress Mega). This is a map that never made a comeback in Tf2 OR TFC so it is likely fairly unknown. It is based around the movie of the same name and is basically a game of CTF with a few differences. Basically the two sides were guarding identical prison complexes. Simply crossing the no mans land between the two was a treacherous task and breaching the outer perimiter was a tricky affair thanks to the usual placement of sentry guns (and the Sentry Guns in TF Mega were far more powerful than the pitiful ones you see in TF2. As a general rule, if you heard them activate, you were already dead). Supposing one could get past THAT, they had to cross an open courtyard (generally covered by snipers). Should an intrepid attacker make it THAT far they had to retrieve a key, cross the courtyard AGAIN, run past the enemy spawn and insert the key into a nerve gas dispenser and then run to the safety of a chamber. Anyone who did not arrive in time would be killed by the poison gas that flooded the level. It might sound impossible but this was of course in an era when spies had grappling hooks and would constantly pepper defenders with hallucinogenic grenades, demomen had mirv grenades, engineers could build flying drones and scouts had a jetpack!