At this time there is no complete list of all the accessible pharmacies in Berlin available. Most pharmacies, however, are accessible or have a doorbell so that a wheelchair user can alert the staff. The schedule of which pharmacies are offering 24 hour emergency service on a give day can be found here:  http://www.akberlin.de/notdienst.html
When in doubt, we recommend that wheelchair users call the pharmacy in advance to inquire about its accessibility and if need be, to let the staff know in advance that one is coming by.