Thanks for your enquiry. I will endeavour to answer your request in stages. There are multile solutions to what you have asked but they might not exactly fit the model you have outlined. Also it maybe that I have not properly understood your requirement. Whilst we recommend the Joomla 3 version there is also a Joomla 2.5 version but which is no longer being upraded. All the facilities I mention below are in the 2.5 version.
One thing however is that it will be necessary for users to login as that is the only realistic way of knowing who is the current user. It is also necessary in order to protect unauthoised people from downloading.
We have an over 1000 members of an organisation. Organisation wants to give download paper of journal for free only for organisation members but not all the papers once at a time.
From the above I understand that the usual method is an individual download button per Download. This is the default situation with jD.
Suppose the member of an organisation has already registered with site and want to download the any year paper then organisation wants to put a two fields username and email after clicking on Download button and after checking their authentication only with username and information like password for pdf (We have encrypted pdf with password) and pdf download link of respected article will be sent to entered email id without log in.
From this I understand that you wish to allow certain users to be able to download say a zip file with all 4 issues of a particular year, or maybe a pdf file that combines all 4 issues. This is feasible with the correct arrangement. There are several possibilities. In the following I will presume that you have already made the combined Download, but note there is a mode where jDownloads presents 'tick' boxes to be combined into a zip 'dynamically and for this zip to be downloaded. But I think this 'tick' method would not match your 'security' arrangements.
The simplest scheme that comes to mind is that jD supports individual passwords per Download. Thus if the user is advised of the password then they will be able to download. There are other mechanisms such as Alpha User Points where each Download has a 'price' in points and you can give the user points but that seems to me to be too much administration for your model. Whilst mentioning things you can protect Downloads with a Captcha.
The key is of course the email or similar for the user to request and for you reply to the user with a download password. The best way to do that is with a separate plugin extension. Note that plugins can be included in jDownloads 'descriptions' so it would act as an integrated whole. When your admin gets an email then one action could be to add them to a specific Joomla User Group (UG). This could be a UG that allows them to be able to access (see) and download any 'Annual' Download or a to have a UG called say 'UG1969' which would only allow access to the 1969 combined file. There are of course many variations of this theme
On the reporting side jD has an accessible and downloadable text based Log file that reports all activity. In addition it also optionally supports an email for every download from the front end and also a separately worded email for every upload from the front end.
So I think jD can support your needs but in a slightly modified way to your original 'spec'.
Please let me know if you need any more info. We would of course assist with any jD queries.
There is a lot of documentation at http://www.jdownloads.net/