If you do a complex work you will probably have to deal with a lot of documents containing internal or external hyperlinks. In this case, a tree structure is very good to store them (for example file-systems or the web use trees). I will summarize the good and bad points of some free Linux softwares that I used to accomplish this job.

Cherrytre

 

Tree structure : good
Documents storage : local files-system, one big file (XML or database, crypted or not)
Working in group : bad, one big file so no conflict management
Import : good
Export : bad, a pdf export but without index
HTML export : poor
Links : good, update links if a target is moved
Lasting quality : a personal development, less used than zim, but a good and attractive software working on Linux and Windows.
Other good points : allow encryption, manage attached files, reliable
Other bad points : having all the documents in one big database is scary even if cherrytree is reliable.

Zim

 

Tree structure : good
Documents storage : local files-system, one file per text
Working in group : good, one file per text so you can use git, integrated git module
Import : poor
Export : not bad
HTML export : good (a template system is used)
Links : good, update links if a target is moved
Lasting quality : active mailing-list, seems good, three times more used than cherrytree
Other good points : tag system, back-links informations, manage attached files
Other bad points : some characters can’t be used in titles, reliability is not perfect but documents are split and we can’t loose a lot, you can’t nest styles.

Mediawiki

 

Tree structure : you need to work with an heavy discipline
Documents storage: web server, database
Working in group : good
Links : bad updating system when you change the title
HTML export : it’s an html software
Export : poor, actually no PDF export
Lasting quality : perfect (it’s the software behind wikipedia)

Docuwiki

 

Tree structure : almost good, need a bit of discipline
Documents storage : web server files-system, one file per text, no data-base
Working in group : good
HTML export : it’s an html software