I think the easiest method for storing loose ponies is under bed storage... however I'm not sure if they are tall enough to store G1 ponies.
For my G3s, I first grouped them by pose since they fit nicer side by side and I wrapped any that would bleed (especially my divine shine gooey ponies) in tissue paper before standing it next to the others. Then I filled each bin as much as I could without squishing the ponies and then filled in any gaps with packing paper. The bins I got also have wheels on the bottom so they are super easy to move around and they stack nicely too. Locking lids is a good idea too.
Here they are stacked..
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loginAnd here's what the inside looks like:
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loginthey also fit MIB G3 singles very nicely too...
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loginAnd for larger boxed items I use large bins..
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loginGood luck and happy pony packing!