Good point!
One can set preferences locally using Style:
Style[Plot[Sin[x], {x, 0, 6 Pi}], NumberPoint -> ","]
Another option is to use BaseStyle:
Plot[Sin[x], {x, 0, 6 Pi}, BaseStyle -> NumberPoint -> ","]
or TicksStyle:
Plot[Sin[x], {x, 0, 6 Pi}, TicksStyle -> NumberPoint -> ","]
All the above methods allow to display commas in axes ticks instead of periods.
HTH,
Alexey