Can Darkseid's Omega Effect option 3 work on a colossal? If Darkseid hit the colossals defense would he be able to put it in another square?

Yes. I have done this. It's hilarious.

Just make sure to put the colossal's entire base within his range.

From the Player's Guide:

Greatest Move Ever. It can change the outcome of a battle royal in a hurry.

I like to lasso punch Anti-Monitor

My son played Anti-Monitor in a 1000 point tourney and got creamed by that effect. Its an awesome move if you can make it work.

While on the subject, does option 2 work against Colossal figures who are immune to Exploit Weakness and Psychic Blast? Example is Anti-Monitor, who is immune to Psychic Blast, Exploit Weakness, and "powers that replicate the effects and grant those powers."

Check with your judge, but I know all three judges I have played under allow "Penetrating Damage" to be different than Psyblast/Exploit, even against Colossal figs.

It absolutely does work. DARKSEID WILL NOT BE DENIED.

You have to read the text of each colossal character carefully. For most, they will not be immune to Omega Effect Option 2.

From the Anti-Monitor Rules:
For the Anti-Monitor for example, the ability, power, or effect must either 1) reproduce the power or 2) allow it's use.

From the Blackest Night PAC:
From the Player's Guide:
With regard to reproducing the power, Omega Effect Option 2 does not do that since it modifies the damage value by -2. Penetrating/Psychic Blast does not modify the damage value by -2. With regard to allowing him to use the power, the word use (which is a Heroclix game term) is never used in the description of Omega Effect. So he does not use it. For those reasons, Anti-Monitor is not immune to Omega Effect like he is immune to Penetrating/Psychic Blast.

Now whether Thunderer of Qward and Qwa-Bolts Option 2 reproduces Penetrating/Psychic Blast is a good question.

From the Player's Guide:

It is a good question. Off-hand, I would probably rule that it is not a reproduction, but I would not be hard to be convinced otherwise. Here's my thinking...

The "reproduction" part of the special figure rules was always meant to cover things like "Stealth" versus "Batman Ally" (from back in the says when Batman Ally was not using Stealth).

Now, if Qwa-Bolts was "reproducing" the effect of Penetrating/Psychic Blast and the intent was for Anti-Monitor to therefore be able to ignore it, then it would have been much much simpler to simply state "Anti-Monitor ignores penetrating damage." It would have been much clearer and more intuitive for the question at hand. Between that fact and the reality that we players have experienced - that these rules have often been tweaked and not looked at with a hard eye for rulings that have come down (until Dr. Manhattan, that is) - I feel comfortable with that ruling being inline with the original intent.

So given the way modern effects are worded, I assume that language is just a holdover from days gone by and essentially meaningless?

The only thing I can think of that this would apply to would be Shape Change versus Skrulls/Danger Girl

Thank you for mentioning that (since they actually are slightly different than Shape Change.) Unfortunately, this also means an errata to clean things up will probably not be forthcoming.