Students have used a variety of software for taking notes. The most commonly recommended are: OneNote (PC Only), PowerPoint, Adobe Acrobat (Reader, Professional, and third party options), and Evernote.
OneNote (PC Only) can convert handwriting to typed text to facilitate searching notes without typing (although you can keep notes in your own handwriting). It provides a structure for organizing pages, lectures, courses, and books. (Since the presentation of material is designed for the computer, you should try to avoid putting notes in the margins, which will not print without a lot of re-formatting.) OneNote files can be synched between computers, which is useful if you have separate tablet and laptop devices.
PowerPoint is part of Microsoft Office and some students take their typed notes directly in PowerPoint’s note view. The obvious advantage is that it normally comes bundled with Microsoft Office, but is really only designed for typed-notes. Inserting - or adding to - diagrams can be difficult.
Evernote (PC or mac) is both a software and web service. It has the advantage that notes are available from any computer with the software installed. There is a free trial version that will probably not suffice for extensive medical school notes. There are other services similar to this and it is best to shop around if this is the method of choice.