The deadline was March 31st, but has now been extended to April 12th: http://europa.eu.int/comm/internal_market/indprop/patent/consultation_en.htm
This is probably in no small part thanks to FSFE's associate organisation FFII, who also have a website with useful info about this consultation: http://consultation.ffii.org/
If anyone is stuck for time, they could endorse FSFE's response, and if they have time, they could add comments or examples of there own.
A html copy of FSFE's response is now at: http://fsfeurope.org/projects/swpat/fsfe-patstrat-response.en.html