Notes and Highlights in Ebooks

This is my first post here, so I will apologize in advance for the naivete of the following questions. We all have to start some where!

I am interested in developing a website and was drawn to O'Reilly for a number of reasons, including the ability to purchase DRM-free ebooks. I wish to keep all of my purchased reference material in electronic format, if possible, for accessibility, archiving, and the ability to make digital notes and highlights in the text.

Unfortunately not all of the books I am interested in acquiring can be purchased on the O'Reilly site; some are available on Amazon, yet not all are available in electronic format. At least not yet.

My questions:

1) I want to purchase ebooks to read on a laptop, with the ability to make notes, highlight portions of the ebook, and cut-and-paste code examples (which this site already states is possible).

Can this be done with all the DRM-free formats supported by O'Reilly?

Case in point. I downloaded a sample of a particular book to determine if these tasks could be accomplished.

In a pdf file format, using a standard Adobe Reader 9, the highlighting of text and the ability to make notes is not permissible.

Is this simply a limitation of Adobe Reader 9? Would these tasks be doable in higher-level Adobe Acrobat Standard, Pro or Pro Extended versions?

2) Is there any way to do the same tasks (i.e., notes, highlights and cut-and paste) with Amazon-based Kindle books? Can the Kindle format be saved as a non-DRM pdf or other type of format that would allow the aforementioned tasks?

3) If not Amazon, are there other sites that offer technical DRM-free ebooks that would support the tasks outlines above?

Your consideration is very much appreciated.

Patrick Jerome