i found setting up the traps was one of the most fun parts of the game, especially when you link different traps and send agents crashing from one trap to the next. So as not to kill my own minions i would have a main corridor leading into my lair and have a door leading to another corridor which was loaded with traps. Using wind traps to blow agents into other traps and further along into my corridor of death was great fun. My main corridor into my base led to my security room, so any agent that decided not to try the door and take the trapped corridor was met by a friendly hail of gunfire.
Damn i wanna play it now, will havta re-download from GOG
Just checked out your screenshots, where you have placed the barracks i put my winding, trapped corridor. The barracks i have at my base centre with the dining counter and lounge areas mixed in.

I'm still on the first island at the moment, so I don't really have the space to put in long decoy tunnels in the mountain.
However what I have done seems fairly effective -- I've built a bunch of topside shacks, installed popup traps in them, and then locked them with a level 3 door. Most of the agents who visit my island head straight for the shacks, break in, get confused by the popups, and then stand around looking confused for several minutes. After a couple of times doing that they leave the island and my heat goes down. :)
Occasionally some of them will come in the main base entrance; I've mostly got barracks and lockers around there so there's nothing too exciting, and there's a small gauntlet of popup traps to wade through before they can get to anything dangerous. It's not perfect though because that's high-traffic so if the agents get that far the popups usually take out a few of my own minions as well -- but they're nonlethal so they just need a few minutes to recover. But I try to tag any agent who starts getting too close to the inside for weakening anyway, which helps.
I did also set up a trap zone in the far corner of the mountain (mostly for fun, but it also seems to raise money a bit); it's basically just two entrances with short corridors (filled with level 3 doors) leading up to a square corridor filled with wind traps. Usually the agents will break through one or two doors before getting bored and leaving; occasionally a squad will be persistent enough to make it through to the square corridor, at which point the wind traps will blow them around and around until they die. Originally I had it completely disconnected from my base, but I've since put in another corridor of doors (and cameras) to make it easier to clean up the body bags in between (and avoid having my minions carting body bags around on the surface, which disturbs the tourists). So far I haven't had a break-in through the access corridor (though I have to keep it locked at level 3 to stop my minions from going in too early to claim the bags and either getting hurt by the wind traps or disabling them for the agents; I drop the level only when it's safe to clean up).
Of course, I haven't unlocked any super-agents yet, and I try to keep my heat low so I don't get agents any better than "good" level (and most are "pitiful"). Not sure if this strategy will hold up if superagents start knocking.

like what uecasm said, making tons of dead end alley ways with traps is good to kill off any agents. But if you do not have the cash to make tons of traps, confusion ones just work as well because
1.) Doesn't kill anyone, so your henchmen will only be confused for a while
2.) Reduces a lot of heat, once they are weak and confused send a "Social" minion over there ( Spindoctors work wonders) to kiss their a** (so that the agent simple goes home and reduces heat).