Docear
免費軟件。Docear的優點是可以自動提取PDF中的highlight，并且整合了開源思維導圖軟件。開發的起初就是為了寫博士論文，通過文獻閱讀和管理，生成思維導圖，從而直接用來寫博士論文。
可以將PDF中的標注和PDF與論文章節相關聯

Citavi
可以將PDF中的標注和PDF與論文章節相關聯
免費版只支持100條文獻內容

Qiqqa
支持在windows系統上在指定文件夾的PDF中進行搜索

DEVONthink Pro Office
支持在Mac系統上在指定文件夾的PDF中進行搜索

Histcite
Histcite 是一款文獻引文分析工具，通過數據分析，可以快速繪制出某個研究領域的發展脈絡圖，讓你找到重要文獻和學術大牛。

Zotero
免費的文獻管理程序，安裝ZotFile后，可以手動(無法自動)提取PDF中的標注內容，但是無法將標注內容與論文章節進行關聯。
可以和Dropbox整合，進行同步

Sente
This feature is also available in Sente. The idea is: you quote a certain sentence or paragraph from the PDF; then, give a title which summarizes the core point of the quote and tag it if you want to. These quotes serve as a short summary of the article. The titles are your reminds of the core points of the quote. It is like summarizing the summary. Very neat approach to reading articles. The neat part in Sente is each of these short quotes could be exported as a separate note file. That means, if you have 20 quotations from the article, you will have 20 short notes: titled appropriately in a folder in finder.