Depends on how rich your villain is. Tungsten is a moderately expensive metal ($15 per pound) that combines extreme density (20 tons per cubic yard) with extreme durability that can be used in lair construction. Here's a nice layout;
5 ft of tungsten would have impervious toughness 21 and built without weak points (rolled homogenous construction) they'd be immune to criticals. Tungsten is also extremely energy-resistant so you can justify Immunity 10 (energy, half effect) on your walls. That should considerably slow down your heroes when attacking the lair and force them to go along the normal corridors instead of crashing through walls in a direct line and avoiding the other traps.
The simplest is putting large antitank mines all over the place. This is damage 14 but it's also messy. You can also apply a really large electric charge to the ceiling and floor, just a bit less than would be needed to close the circuit through air. This works like those insect traps with the electrified bars that have a lamp to lure insects in between the bars. The insect is significantly more conductive than air so when it passes between bars, the energy needed to close the circuit becomes suddenly less than what the bars have and you get a tiny lightning bolt through the insect, which is blasted apart. The same applies here only the current is much bigger and there are heroes instead of insects.
This electricity trap has several advantages. First, it keeps working as long as your base has power - the heroes would be hit with damage round after round without expending trap ammunition. Secondly, it doesn't make a mess of your base like a big mine would. Third, the heroes themselves are what closes the circuit and they draw the lightning through them - no dodging it (damage is perception). Fourth, it doesn't matter if the heroes wear invisibility cloaks or use smoke and flashbangs to provide concealment like in typical SWAT raids; the trap still works automatically if something closes the circuit. So it is a good method to repel attackers that minions with machineguns wouldn't be able to see at all. Fifth, the trap has neither a delicate trigger mechanism nor relies on any kind of complicated controls to function - it's just a pair of room-sized electrodes in the form of ceiling and floor. Thus it cannot be disarmed or easily destroyed (the electrodes will be of the same composition as the walls) and stopping it would require cutting off the power supply (which would be deeper into the lair itself and hence defeat the purpose of disarming)
Put a 100x100 ft large chamber in your lair. This will still be a big electric trap like the corridors but it will have a double ceiling. The real ceiling will be 20 ft higher than normal and the lower part will be detachable. Once the heroes get in and start smashing into the inner gate to go further, you unlock the ceiling and it falls. This has two interesting effects;
1) First and foremost, falling damage. The ceiling weighs 120.000 tons if made of tungsten - a bit more than a Nimitz-class supercarrier. That's mass rank 23 so it deals 23 falling damage. Since it is the room's ceiling and fits the room exactly, there's nowhere to dodge so it hits automatically. SPLAT!
2) Secondly, it's the weight. Even Superman is barely capable of lifting such a massive weight - anyone less strong would be unable to lift the ceiling at all so most heroes (or even teams of heroes) are automatically pinned beneath it. And while pinned, they keep taking electricity damage from the electric trap and potentially crushing damage from the sheer weight. A couple rounds later, they're toasted.
No good lair is without ovens. They're useful in disposing of dead bodies, annoying minions, functioning as incinerators for the lair's non-recyclable waste, vaporizing toxic or radioactive compounds so they can be spread over the city's atmosphere if your reasonable demands are not met and, naturally, baking. Improving upon said ovens, you put some pipes from them to several rooms you want to trap. Then you load your high-temperature ovens with stone, brick, soil, dirt and the like and melt them to produce "magma" you can funnel into those rooms when heroes come calling.
Leave the front door of said rooms or corridors open so the heroes don't break it in entering but leave the back door closed and heavily reinforced. Heroes go in, you seal the front door and flood the room. This has several effects;
1) Damage. Magma does 18 damage per round of total immersion. That's bad for most heroes. Tungsten melting at twice the temperature of typical magma, it will be unaffected so your base won't take damage (mechanically, 18 fire damage would leave your tungsten walls unaffected due to immunity+impervious)
2) Birthday Suit Surprise Party. The heroes might be able to survive magma for a time. All those gadgets, devices, suits and whatnot the heroes come with? Not so much. It's magma - if it can melt a tank, it will melt Batman's utility belt even if the Bat somehow survives.
3) Drowning. A need to breathe is counterintuitive if you are submerged in most liquids. Magma is especially bad in this case. Not only you can drown in it but it is also substantially denser than water and thus harder to get out even if you survive inhaling it. And if you're unlucky enough, it will cool down before you get rid of it, solidifying inside your respiratory track. That's probably bad.
4) Entrapment. The heroes can survive the magma attack? No problem. Engage the attached cooling system and freeze the magma in what it was before you melted it down. If you used dirt and rocks, the heroes are now trapped in 20-ft-thick solid rock. If you used stuff from the scrapyard, the heroes are now trapped in 20-ft-thick solid iron and nickel.
You can't have this kind of area damage traps in your inner sanctum, seeing as they are nondiscriminatory. OTOH, you could have more standard stuff. The GAU-8 Avenger is a good rotary cannon usually mounted on the A-10 Thunderbolt aircraft in the antitank role. It shoots 30mm tungsten carbide shells that can penetrate tank armor (damage 10) at a rate of 60 shells per second (multiattack+improved critical), turning most targets into Swiss cheese. Get a couple dozen of them, automate them and have them shoot the heroes all at once.
If the heroes manage to overcome the traps, make for your quick escape route after removing the safeguards from the lair's main reactor - the one you were using to power the electrified floors and the high power ovens and your mad science experiments. Set it to blow up in a multikiloton nuclear explosion and don't worry about the radiation. The consequetive layers of tungsten walls in your base act as anti-nuclear bunkers, containing all but the most powerful nuclear blasts so the city won't be leveled. Tungsten is also significantly denser than lead so it stops radiation a lot better and it is also conductive so the layers of walls will function like a huge faraday cage, trapping in the explosion's EMP - so both you and the city's inhabitants (your future slaves) will survive without problems.
The heroes OTOH, will eat the blastwave, radiation and EMP in a closed environment, suffering the maximum possible results.