These are from a patent related document and I can't understand very well.
They are used like these：
1) 特許庁長官殿 2) 出証意2012
Can anyone help me?
特許庁長官殿 means “Commissioner, Patent Office” with a polite suffix, as you and sawa explained.
出証意 is not a word. From what I learned from the web, I think that it appears in a reference number of a certificate of application documents and acceptance of application (出願書類及び出願受付情報に関する証明書) for a design (意匠) in the form 出証意2012-1234567.
長官 is the top person of that institute. 殿 is a polite affix attached after people's name or title in business or formal occasions, contrasted with 様 used in personal occasions. For the second part, it is not an ordinary Japanese, and my guess is that it is an abbreviated code used for sorting the documents, shortened from something like "出願証 意匠 2012年" "proof of application, classification: design, submitted year: 2012".
証 may stand for something more or different.