It will be better if you create a list of the articles in word or html and link the pdf to it. But  in that case, the pdf will not be searchable.

Qiqqa is want you want. Free. No conversions needed. Autotags and manual tags allow you to filter and find patterns. All text is searchable with the filter. For security it leaves your original PDF untouched, and makes a copy on your PC with your annotations. A paid-for version lets you keep your repository on a LAN. The optional  Qiqqa cloud copy lets you browse from other PCs where you do not have much space. 

http://www.qiqqa.com/70557

Hi,

In technological universities Jotero and Mendeley seem to be popular for managing scientific articles, and in the social science and humanities the Refwork is more popular than others. Most publishers prefer that you write and send your paper as a Word file. The conversion into PDF file is done by the publishing system.

You do not need to create a local repository on PC - you can continue to use Mendeley and save all documents in the cloud.

https://www.mendeley.com/reference-management/reference-manager

if you are using Mendeley then you can also save your data on the web. Even no need to bring your laptop etc. anywhere. You can retrieve the documents through your id anywhere and anytime.

Mendelay and Zotero are good one. Mendley offers the opportunity to sync all your reference list on a cloud-based system and hence it is easier to sync a list on multiple devices.

Mendeley is considered to be the Best