Apple - OCR software for handwritten notes

You could use Evernote for this (Free). Just import all of your PDF's as notes and after some time (you can speed this up by upgrading to a paid account), it will automatically process them and recognize the handwriting. You won't be able to extract the OCR text from the notes, but you can search for it.

Evernote does have handwriting recognition, but unfortunately right now it requires JPG format. It cannot handle PDFs. So your work-around may be to consider converting PDF -> JPG using Preview, etc. and then importing into Evernote for recognition. FYI, the handwriting recognition in Evernote for JPG is decent, but not nearly OCR-level from my experiences.

Also, this post describes a good workflow to use Evernote to recognize handwritten notes.

If you're fammiliar with any programming language, take a look @ ocrsdk.com, it's a website that lets you upload images through web API and sends you back OCRed data. Here's the documentation on handwriting recognition: http://ocrsdk.com/documentation/quick-start/text-fields/ and here are some codesamples @ github: https://github.com/abbyysdk/ocrsdk.com There's a nice 50 pages free trial without any upfront charges.