The way I pack mine varies depending on which series they are:
G1 originals- These old warriors get wrapped in toilet tissue then in bubble wrap and then put in a smallish box so they don't move around and bump eachother.
Vacuum metalized toys- Lotsa tissue, small box like with G1's.
Armadas. These guys are tough so they get put in bags and then in a box which is then filled with packing foam.
Unicron- Put in planet mode, big spikes turned down and rings (in wing mode) rapped in bubble wrap, then uni is treated like a G1 and put in a box that fits him snugly.
BW- They get bubble wrap then separated by tissue sheets.
Holiest of holies (MIB)- Technically they are not MISB they are just MIB because I take em out and play with em then put them back in when I'm done. These Tf's are all in mint condition and are mostly G1's or reissues. I wrap their boxes in tissue (No dents here

) and arragne them in a box.
Now that is the bizzare way I pack my guys