Below is a list of all the suits and weapons that all should fear. Some can just destroy a colony, others can take out the population, and some can do heavy damage to colonies.

Big Zam
Large Mega Particle Gun:
This weapon is strong enough to take out many ships and suits, but not enough to destroy a colony.
Mobile Suit Gundam

Zaku I
Colony Gassing Equipment:
Uses gas to kill the population of a colony, but leaves the colony, weaponry, and suits intact.
08th MS Team

Physalis
Atomic Bazooka:
Very powerful weapon. If fired at the right location on a colony, it could breach the colony wall and cause its destruction. Firing the bazooka does some damage to the Physalis and the shockwave is very dangerous to surrounding suits.
0083 Stardust Memory

Mega Bazooka Launcher
Mega Bazooka Launcher:
A Sub Flight System for the Zeta that is powerful enough to breach a colony wall.
Z Gundam

F91 Gundam
Beam Launcher:
Very powerful weapon with enough power to breach a colony wall.
Gundam F91

Rafflessia
Mega Particle Cannons:
Tightly concentrated on one spot would give it enough to take a colony.
Gundam F91

Victory 2 Assault
Mega Beam Rifle & Variable Speed Beam Rifles:
Either of these weapons on the V2 Assault can breach a colony.
V Gundam

Zanneck
Mega Beam Cannon:
Truly a suit to be feared. This weapon allows the Zanneck to easily take out a colony and also destroy suits on Earth from the Stratosphere.
V Gundam

Gottrlatan
Mega Beam Cannon:
The weapon is powerful enough to take a colony, but whether or not it is like the Zanneck's is unknown to me.
V Gundam

Devil
Nanites:
Really don't like this series, but I'm told that this suit's "nanites" can do the job of taking a colony.
G Gundam

Wing
Buster Rifle:
Not enough to destroy a colony, but could probably do significant damage. Powerful enough to destroy Gundanium mobile suits.
Gundam W

Wing Zero
Twin Buster Rifle:
Whether it's the Gundam Wing or the Endless Waltz Version, this suit's twin buster rifle is enough to take out colonies.
Gundam W & EW

Epyon
Beam Sword:
Quite possibly the strongest beam sabre or sword ever. Destroyed the Space Fortress Barge, which size was similar to that of a colony's.
Gundam W

Vayeate
Beam Cannon:
Stronger than the Wing's Buster Rifle and can fire constantly. Can't destroy a colony.
Gundam W

Tallgeese III
Mega Cannon:
Strong enough to destroy a colony.
Gundam W EW

Gundam X
Satellite Cannon:
A Very powerful melee weapon. Though too widespread to take a colony, the blast is more than enough to take out masses of enemy suits.
Gundam X

Double X
Twin Satellite Cannon:
Obviously stronger than the X's single satellite cannon. If the blast were to his a UC colony's window, it would most likely destroy the colony. Like the sing satellite cannon, perfect for taking troops out at a distance.
Gundam X

Virsago Chest Break
3 Barrel Megasonic Gun:
Powerful enough to destroy a gundanium mobile suit.
Gundam X

Ashtaron Hermit Crab
Satellite Launcher:
An optional weapon, fired by the Virsago Chest Break while the Ashtaron is in mobile armor model. Very similar to the satellite cannons of the X and Double X. The Virsago Chest Break is need for the weapon to fire because of its solar collectors.
Gundam X

Grandine
Long Range Particle Cannon:
Though not enough to take a colony(not only because the weapon isn't strong enough but because this is a ground armor only), good for taking out enemy suits from a distance.
Gundam X

Turn X
Weld-Off/Destruction Manipulator :
A very powerful weapon located on the right hand of the Turn X Mobile Suit. Though I am not certain of its actual power, it is strong enough to take out a ship, much less a mobile suit.
" Gundam

More to Come.