Actually putting them in the safe is one of the best ways. Wrapping them with anything, unless you do some serious prep to the gun (like cosmoline) will usually result in rust. Plain old paper is probably the best if you're going to wrap it with something. Oil the gun up well, and wrap it. The thing with any kind of cover is that the covering will absorb moisture, and then you have a moist cover laying on your gun. Not a big deal if you live in the desert. Big deal if you're in the tropics.
I have about half my guns stored at my dad's. He's all the way out on the west coast. After bouncing around the country, and finally winding up on the opposite end, I've had to leave them there until I can figure out a way to get them back here. They were sitting in a Knaack "gang box" (like the construction crews use). All I did was clean them, oil them, and put them in. It's very dry where he is. The box is sitting on a pallet, off the concrete floor. There are foam pads between each layer of guns. That's it. I visited them about 6 years after I stuck them in there and there was not a speck of rust or anything. He had checked them once every couple years, but there was nothing for him to do. They just sit there and bide their time until I can figure out a cheap way of getting them out here. That was about 3 years ago, and there hasn't been any change.
The biggest thing is to just clean them well in the first place so there is no fingerprint residue. The acids/oils from your body will promote rust. Also any rust that's already there will just grow. Clean them well first.
After cleaning them, oil them well to prevent rust from starting. I think Break free-CLP sells some kind of "Collector grade" stuff that I've heard is pretty good for just this.
Keep them in a dry place. If you already have a safe, you could leave them there and use a rod to dry it.
The advantage to this is you get to actually play with your investment, or at least show it off to your friends (just clean off the fingerprints). Also you're much more likely to notice if you're starting to get any problems faster if you're always looking at them.
Either go whole hog and preserve the heck out of it, or go with a "flyable storage" plan and just look at them every month or so.
Ross