Ooops. Just needs a little positive lookbehind.

perl -le 'for(@ARGV){s/\./,/;s/(?<=\d)(?=(\d\d\d)+(,|\Z))/./g;print}' 
+1234567.89 234567.89 1234567 234567
1.234.567,89
234.567,89
1.234.567
234.567
[download]

update..

Ok.. yours is shorter... mine is probably more efficient for not invoking $& at least :)