As said, 3x Guardians (+Farseer usually) could take them out with good use of Entanglement and Plasma Grenades, the GK's ranged damage wasn't that impressive (after the nerf in the first patch), just decent. FoF/Entanglement prevents them closing melee.
Orks could hide behind buildings guns, and hide in buildings to prevent Shout/P.I. gib (and your standard Big Shootas rush would do a bloody good job anyway). Mek + 'port could save a squad from this too. It was more or less the same story with Guard, but you had to have a Turret and LP2 protected by Mines (preventing melee and they won't take those structures out on ranged with any efficiency). You'd basically box the SM in until you could hit him with something big, eliminate him and win the game (afterall, you had total map control and he had no eco).
As for Necrons, 2x Warrior Squads + the Lord could take them out with little difficulty. In melee.
You had easy access to Flayed Ones who were about as tough for melee anyway.
Often, the trick would be to kill the GK's before they could join up with the Chaplain, as you'd be sitting right outside his RAX (attemping to destroy it) as the GK's emerged. Without the Chaplain around they were easy pickings.