Hello,
in the meantime I've tested some different apps and let you know my experience (if someone are looking as well for a solution with the S-Pen from Galaxy Note 3).
(I got more information from this german forums (if you understand german):
Samsung Galaxy Note 3 — S-Pen als Textmarker (freies gelbes transparentes Markieren) mit Android PDF App — Android Forum - AndroidPIT
Sammlung von S-Pen Apps - Android-Hilfe.de)
and like to write you my summary:
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Skitch from Evernote (free if you also have Evernote Premium account)
not suited because the marking will either be saved as a picture or in other words only recursive deletions of the markings are possible (e.g. if you whant to delete the tenth last marking in order to do this you also have to delete the last nine markings!)
Moon Reader Pro (approximately 3 euro)
you also can't really efficiently mark. You have to tap and then you can mark the word. This app is good as a reader for books because you can set up an speed to train speedreading or listen audio but not really appropiate for student.
I also have Ez Reader Pro bought but it's definitely not the solution!
a) you can not freely mark (like the Airbrush-Tool with waves from hand), you only can mark horicontally but not diagonally or so!
b) you always have go go backward when you want to flip to another page.
PDF Max (approximately 6 euro)
looks like a very professional PDF app like Ez Reader Pro, here it seems that you can only mark letters (words and sentences) but you can not mark freely (e.g. diagonal) as you can do with a traditional marker.

Lecture Notes (approximately 4 euro; Refund possible!; Trial has all functions of Pro Version but two limations (of page number and something with saving))
is an app developped at a university especially for students. with this app (in addition with app "PDF View" which has to be downloaded as well) you can import a single PDF sheet as a picture and making notes with a second layer. It's a good app as an alternative for the samsung app "S Note" (from Galaxy Note 3).
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Papyrus (Pro Variante Test 10 days): looks to be very useful
1.) Choosing the Marking tool
2.) Mark with Pen, scale and delete some notes with finger
3.) Go to another page with button above
4.) Close: Just go back
In fact this seems to be the best app by now for me for reading PDF books and marking intensively with the S-Pen. I know it's not the easiest way, because the last used marking tool is not saved, you always have to repeat step 1.) when you launch the app but conclusive I would give this app 4 of 5 stars.
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Thanks to you all!
Best regards
fluorescein
