Hello, I'm a patent engineer in a multinational firm. Only just very recently we have implemented a standard form for invention disclosures. We don't use a special program, but the invention disclosures are stored on a drive with restricted access upon receipt thereof through e-mail. The date and hour of receipt of the e-mail is noted in a separate file. In order to keep a close watch on secrecy, it is possible to encrypt the e-mail.
Hope this is somehow helpful.