Walking on Broken Glass'sNick. To quote the caption of the linked image, "Why yes, he does keep one namely a paintball gun in his office. For just such an occasion."
TwoKinds: Alaric. From the time Keith was banished, Alaric had been working nonstop, becoming a general, exploiting every loophole in the law he could and writing hundreds of documents, all so Keith would have to be acknowledged by society. Keith is now recognized as the Ambassador for Basitin society, representing their entire civilization to the world.
General Tarquin has learned how to counter many obscure fighting styles in case he had to one day fight somebody who knows one of them. (Though his knowing this specific case was due to Elan's teacher, Julio, being one of Tarquin's more frequent foes.)
Tarquin mixes this trope with Dangerously Genre Savvy, including having written manuals for his guards explaining that there are no surprise inspections, and anyone showing up with that excuse is an intruder.
In Home On The Strange, Tanner tells his girlfriend a few facts about his childhood. When asked why, he says that it's so he can tell her them again if he gets misplaced in time or body switched. The comic takes place in the real world, so this is a bit overprepared.
All the Homestuck universes. All of them. And, for that matter, all the minions of Lord English, though ESPECIALLY Doc Scratch.
Aside from, of course, the kids and trolls. The exceptions can be counted on one hand. If you want specifics, Terezi, Vriska, Aradia, and their Beforus counterparts.
Tycho: Yes, Mr. President? President: What do you know about manticores? Tycho: Goddamn near everything.
The setting of The Adventures of Dr. McNinja is a town with its own zombie defense system. Obviously comes in handy during the Zombie Apocalypse story arc. It makes a certain amount of sense, since the Genre Savvy Dr. McNinja is written by a man whose basic philosophy towards writing is always go forward.
Dr. McNinja also has a barber on speed dial in case of emergencies.
Not quite Crazy Prepared. The Mayor who instituted the zombie defense policy was revealed to be a time traveler who knew it was coming.
Thief from 8-Bit Theater has two clauses in everyone's contracts specifically for winning arguments. The first reads, "Yes, it is," and the second reads, "No, it isn't."
Red Mage, who reveals that he has numerous contingency plans for any unlikely situation. He doesn't use any of these plans, since generally, his allies will just blast or stab everything he doesn't get to first. Though it needs to be said that Red Mage's plans are nearly all undermined by the fact that he doesn't know what he's doing most of the time. He's simply convinced he does.
Zola had her brain specifically prepared in case Lucrezia tries to possess her.Not only is she immune, it backfires perfectly.
Mechanicsburg itself. They have a system that showers the entire town in case they are attacked with poisonous or sleeping gas, and have systems capable of launching entire buildings attackers. Combined with Castle Heterodyne below, and the readers gets a very good impression as to why Mechanicsburg has never been taken by enemies.
This page shows just a small slice of the levels of Crazy-Prepared Castle Heterodyne is. Being prepared for a weapon that stops time and having defenses that will allow the Castle to remain on-line and still able to control some defenses while locked in a stasis field where time is frozen takes this trope Up To The Eleven.
Parodied in Skin Horse, where UNITY has spent a great deal of time planning strategies to fight historical figures. All of them consist of, "Look a (something historically connected to the person in question)! Leg sweep!"
The protagonist of Geist Panik has a display◊ which features: a water gun in case of witches, a stake for vampires/tents, the sonic screwdriver for use against both Daleks and shelves, a crowbar for headcrabs, a fiddle in case of Satan, a nail-gun in case of Jesus, and a huge ass-gun in case of zombies/raptors/misc.
In Casey and Andy strip 649, Quantum Crook is prepared for Quantum Cop despite not knowing he's also in 1886. Quantum Cop is prepared for Quantum Crook being prepared...
NASA in Daisy Owl is running a Space School on the moon to train grown Space Babies for fighting off aliens. They don't know of any aliens existing yet, but better safe than sorry!
"We need stronger firepower to stop this guy. Didja bring the bazooka?"
"Check the glove compartment."
On the next page, the villain diverts the heat seeking missile with a molotov cocktail he happened to be carrying.
Vlademyre Hynner from Mortifer has this in spades, to go along with his genius IQ. Best exemplified on this page, complete with Lampshade Hanging (Warning: Spoilers!).
In Spacetrawler, Growp tries to kill Emily in her sleep, only to find there's a decoy in her bed. Emily had set this decoy up even though she could not have possibly known beforehand that Growp was coming for her.
In Crimson Dark, Sarah, former controller of Espenson Station, is able to quickly take over the station's computer systems when Whisper, the other resident computer genius, disables the anti-wireless jamming in Sarah's cell. It turns out that Sarah leaves back doors in every computer system that she ever works with, because you never know when an employer will try to screw you over.
In Chaos Theory, Kevin's suit contains every explosive device known to man, and is rigged to explode if he so much as twitches in the wrong direction.
Sunstone it seems that Ally is equipped to handle many different fetishes and situations that arises if ever she found herself in such a relationship, despite being too shy to seek out that kind of thing for some time. Lampshaded in a strip.
Lisa: I thought you weren't into Pet Play?
Ally: I was never in the scouts either but I still stick to the ''Always be Prepared" motto.