You'll generally want the Explosives Perk to deal with the hideously over-tuned Super Mutant Primus and Mythic Deathclaws for fights where you can't secure a stealth-kill or -cripple, or go heavily into the Heavy Weapons Perk and the Explosives Perk to max out the damage on a rocket launcher or fatman for when you absolutely must ruin something's day in a single hit.
Otherwise, a fully tricked out .44 pistol is great for picking off small fry or dealing some lethal damage in close range, the 10mm weapons tend to not do so well past level 80-ish unless you've got the right Companion Perks and/or a singular pistol, the Deliverer, which allows for some hilarious amounts of V.A.T.S. sniping from stealth.
Gauss Rifles, fully charged, can one-shot a great many things and failing that, can do ludicrous amounts of damage to highly armored targets.
An Explosive, Plasma or Wounding Assault Rifle or Automatic Combat Rifle can dish out hilarious amounts of pain and suffering to whoever you don't like at the time, and with Explosive weapons, their damage does scale up with the Explosives Perk, so that's fun.
I'm not sure if the 'Science!' Perk does the same for energy-based weaponry, or only those useless Gamma Guns. That said if you're aiming to kill off groups like the Brotherhood or the Railroad, a sufficiently advanced Gamma Gun with the Human-Bane Legendary Tag is ridiculously powerful and capable of one-shotting all but named NPCs or Power-Armor troops.
Melee is disgustingly effective, especially if you go for Swann's fist weapon for the fisticuffs-loving character, or a Furious Power-Sledge or the Baseball Bat from the Jamaica Plains quest. And let's be honest, using the Pain Train Perk plus a Furious Melee Weapon is just ridiculously fun. You knock just about everything over and deal insane damage, and then you get to beat on their asses as they pick themselves up while your Companion also gets some free hits in.