Is selling empty beer bottles to regular shops and supermarkets halal or haram?

If you were to sell them to someone who would not use them for unlawful purposes, then there is no harm in that. However, selling them to someone who would use them for unlawful purposes, such as filling them with beer, is forbidden because it constitutes aiding in sin and aggression. If you are in doubt about their use, the ruling depends on the preponderance of your assumption. If you predominantly assume they will be used for unlawful purposes, then it is not permissible to sell them. You can ask shop owners to clear your conscience regarding your religion.