Neutrals are Transformers who have renounced the ideals of factions or refused to take part in the Civil War. While some Neutrals resist joining a faction by choice, some defining themselves not by faction but by world, as the war drags on, the majority are those who are unsuited to combat, such as the Empties.
Marvel Comics continuity
(Events from the UK-only comics are in italics.)
During the evacuation of Altihex, twenty to thirty Neutrals took control of a building, arguing for both Autobots and Decepticons to end the War, renounce their allegiances, and unite. Skywarp took a moment to consider whether or not to take advantage of their idealism - then decided to slag them.
There would seem to be some Transformers within the Transformers Animated series who are neutral towards the conflict between the Autobots and Decepticons. While the Autobots have blue optics and the Decepticons have red optics, these Neutrals are usually depicted with yellow or purple optics in order to set them apart. Two notable examples are Scrapper and Mixmaster, who kept going back and forth between the two factions before having their memories wiped by Bulkhead (but went with the 'Cons for a while, since they had better oil). In the branding rite that officially made them Decepticons, their optics shifted to the traditional red. Lockdown and Swindle seem generally neutral, but they often side with the Decepticons because it's more profitable. Soundwave was neutral and had yellow optics when he was just Sari's birthday present, but later chose to be a Decepticon. While Wreck-Gar was generally neutral, his optics were blue to start with - but he did seem to be good at heart.
Ever since the Autobots and the Decepticons fought each other, the Neutrals prefer not to participate in the war, just to defend themselves.