I don't know about the "new" EU members, like Poland, Czech Republik, Slovenia etc., but between the "old" countrys, like France, Germany, Italy etc. there aren't checkpoints anymore, just signs "welcome to...", but this doesn't mean that the border patrol doesn't exsist anymore, specially the border between the Netherlands and Germany is still protected by patrol cars that stop travellers at random, to look for drugs and illegal imigration.
The Swiss-EU borders still exist in their old form, with manned checkpoints.
Thanks for the update on that, DTS. After consulting my map to see where I was, the 'deserted border checkpoint' I was referring to was on the A64 / E44 between Trier and Luxembourg City. This was a few years ago so they may have dismantled that gate complex.