I can’t really see a big difference other than signtool is newer and requires different file formats for your digital certificate?
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They both accomplish the same thing — code signing. As you pointed out, the principal difference is that
signcoderequires the private key and software publisher certificate to be in two separate files (.pvk, .spc).The more modern
signtoolrequires that they are contained in a single Personal Information Exchange (.pfx) file. (You also need the .pfx file format to use the Association of Shareware Professionals’ PAD signing toolkit.)