My firearms are stored in a safe in my basement (unfortunately) with a dehumidier/Goldenrod depending on the time of year. A dehumidifier is also ran in the basement outside of the safe and kept around 45-50% humidity. Each time I take a gun to the range, it's gets cleaned and oiled. I looked closely at some of the guns, and sure enough, there are small rusty areas on a handful of them in miscellaneous areas.

First question: What is the safest way to remove the rust? I'm reading dry 0000 steel wool. Has anyone done this before without causing damage and actually be effective?
Second question: What other methods of prevention are there? Try to oil the guns ore frequently? Use those silicone impregnated socks? I remember reading to not keep firearms in cardboard boxes or anything similar. Is this true?

Asking about rust removal is like asking what's the best dog/truck/steak/BBQ/chili: everybody has a favorite and those who do not agree are forever damned to the inner circle of Hell and nobody should listen to them lest they, too be damned. There are myriad ways of getting it done without damaging the gun, and twice that many ways of removing rust and damaging your gun.
That caveat aside:

As to rust removal, I have always had good results on light rust using a very light oil and (in order of aggressiveness) my finger, a hunk of wood, or bronze wool (or copper wool, aka chore boy), with 0000 steel wool (oiled) if all else fails.

As to prevention, wax often works better than oil. Regular old Johnson's paste wax in the yellow can. Others will have alternative favorites.
Apart from wax, a thin layer of grease like RIG prevents rust better than oil. Cosmoline...well, we all know how awesome cosmoline is, and it might just be a viable option if you have some safe queens. Besides, it smells good.

If you're seeing rust in areas of handling, consider getting some white cotton gloves. You might have acidic sweat.

Finally, drop your humidity to about 35% and get some air circulation. I use a tower fan along with a bigass dehumidifier.

This was very helpful. Thanks for the reply. I'll certainly give your methods a try. It broke my heart to see so many rusted, and I just want to return them back to how they were a few months ago.