These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Toni Cipriani certainly deserves a mention. Toni is a righteous man who delights only commit atrocities because just follow orders? Or he is a Complete Monster? This theory is quite credible, because Toni is probably the protagonist who committed the greatest atrocities canonical, including killing a man with an ax and carrying his remains to a butcher shop, and this was done intentionally and not to follow an order, without mention several atrocities that go by Donald Love and Ned Burner's orders. While still repents of his sins in a confessional, he never sought redemption when he bombed the area of Fort Staunton.
Complete Monster: In order to get cheap real estate, Donald Love commissions Tony to blow up the Little Italy portion of Staunton Island from underground. Though this explains the existence of the construction site in GTA III, one would think a tragedy of such proportions would be mentioned at least once three years later.
Ned Burner who, under the guise of a priest, makes Tony commit several other atrocities.
Paulie Sindacco this could count as well. In addition to possibly killing the cousin of Salvatore, his methods for killing are pretty brutal, kidnapped Maria Latore (who knows why), tried to bomb the Leone's casino and kidnapped and tried to kill Salvatore in a crusher.
Moral Event Horizon: Paulie Sindacco intersects with the attempted murder of Salvatore, sending his henchmen to take him to the crusher.
Toni's mother has probably crossed with the attempted murder of her own son for not being a man.
That One Level: The game ramps up the difficulty for obtaining some of the hidden packages to an almost insane level. A hidden package located on top of a gas station roof in Portland is considered particularly difficult to reach, and even Guide Dang It assistance if unhelpful.