Yes I'm also sceptical about using EndNote for pdf notes since it can't really do margin notes, underlining and so on on (or overlaying) the pdf pages, right? It can connect separate note files and pdf files in its bibliography database. But maybe the best solution will be a tagteam of Acrobat and some database/organizer tool and so maybe EndNote could be that tag partner.
Endnote can't open the pdfs for viewing or editing - it relies on your default viewer to do this. Endnote does allow you to make notes and lists of keywords that are tied to the library record for the pdf, but as these are part of your Endnote library, they have nothing to do with the pdf. The only way to share your notes would be to share the Endnote library, but that relies totally on the other person/people having a recent version of Endnote installed (8 or higher) if you create your library in the latest version. The only other thing Endnote does is to give you the option of storing the pdf as part of your library. This isn't necessary as you can also link to the pdf's location on yourharddrive from within the library record,but this means that the link will be broken if you open the library file from a different location. This is only an issue if you, like me, use Endnote to find references and like the convenience of being able to open the reference as soon as you locate it in Endnote.
A cheaper alternative to both PaperPort ($199 for the Pro version) and to Acrobat Pro ($400 or so) might be something like
FoxIt Reader - it will allow you to annotate and highlight your pdfs and there are a couple of shareware upgrades that extend these capabilities. I don't have any experience using these features and don't have FoxIt installed at the moment so can't test this for you right now. Check out the "More PDF Tools" links in the lower left pane of the page I linked to...
As I started writing this, I *thought* Foxit software was charging about $20 for each add-on but I see now that they are $60 - $100... At those prices you might as well look at the serious contenders in the non-Acrobat PDF category -
Scansoft PDF Converter Pro,
FinePrint PDF Factory (scroll down for the additional Pro features),
Jaws,
Nitro, etc. The pricing point for all of these seems to be in the $50 to $100 range, depending on whether you go for the standard or pro version. Just as a final note, you can get eXpert PDF 3 for
free with the option to get the upgrade to the new version at a reduced price. It looks like the free version will do what you want, though.