Software designed for managing research and information or for writing often incorporates note-taking capabilities.
Scanning is not enough. To be searchable, PDFs must be OCRed (Optical Character Recognition) which means that the pdf "image" is rendered into text.
Adobe Acrobat Pro has built in OCR.
OCR is also available more or less free elsewhere though quality and features vary:
OCR is almost never 100% perfect.
For highest quality OCR and also foreign language OCR, try ABBYY.