I assume when using ammonia or ammonium hydroxide with the silica gel? I understand your question to be about the use of ammonia or ammonium hydroxide with a mobile phase. It is usually added to the more polar solvent in a solvent system (the most common example, by far, is dichloromethane and methanol; the ammonia or ammonium hydroxide is added to the methanol).

This solvent system is generally used with basic compounds; it raises the pH so that the compound remains as the free base which is uncharged, and elutes easier off the column in less polar solvent systems. Adding base also "deactivates" the silica because the ammonia interacts with the silanol groups on the silica. People will add ammonium hydroxide to the methanol, or will use methanol containing 2 or 7 molar ammonia pre-mixed (these are what I remember seeing available commercially).

another common basic additive is triethylamine (TEA) and this is usually used with hexane/ethyl acetate solvent systems, or solvent systems less polar than dichloromethane/methanol. I will add this to both the hexane and ethyl acetate since there is no miscibility issues that I've found.

A couple of caveats when using such solvent systems:

I usually run TLC plates first to determine if I need to add any additives.

Jack Silver has given a good answer to your query.  Since silica is acidic, so any basic moiety, especially amines (primary, secondary, tertiary) tend to 'stuck' inside the silica column and do not come out. Many times, elution with pure methanol  also does not work. Hence, it is better to neutralize/basify silica either before loading your compound by wetting the column with TEA/hexane or, once you have started the column, you can add 1-2% aq. Ammonia in your mobile phase (MeOH/CHCl3).

To avoid amine additives, reflux the silica gel in methanol with 5-10wt% K2CO3 relative to silica for a few hours, cool, and filter off the silica, and wash with a bit more MeOH, then dry under vacuum at 40C.  Obviously you could also try and just use basic alumina gel as well.

I generally use triethylamine. It deactivate silica with good result for acid-sensitive compounds (like thiol or ethoxyethyl protected aldehydes or alcohols) which have tendency to fall apart in silica.

If compound is sensitive to acid, put 1-2 percent triehylamine in your solvent system to neutralized acid in silica gel. The Rf factor might change.

Yes, generally triethylamine is better to use deactivate silica, before loading your crude compounds to purify.