Best Way To Store Old European Junk Coins?

I would just put them in cardboard flips, when you buy them by the 500 they are a couple of cents a piece

Depends on the specific coin
1. for many countries I have album sheets where I put one of the different types in
2. surplus (ie duplicates or other years) go into a little box for the country
3. more valuable coins go into 2x2s

It is always worthwhile checking in the cataloque if the coin might be of some value.
There are minor varieties which can be quite valuable, eg for australian coppers.
Also you can have pleasant surprises, dealers often don't care much about small change from foreign countries even if they are top quality (aEF or better). To mention just three of those I found in a 10c or 20c junk box: Switzerland Rappen 1868, Netherlands 1/2 Cent 1869 and Norway Ore 1877.
Don't forget that for a dealer it's not worth the time to check every coin in the catalogue when there is only a low chance that the coin might be of value.

Use some pliers to squish the staples flat. Then it is very difficult for stacked 2x2s to damage each other.