Well I hope someone can share their experience  :)
The html rendering is not the most important feature to me but that the desktop program can generate direct links to your files with urls having the same path as on your harddrive. My guess is that most of them generate encrypted links and redirect to pages.

Personally, I can recommend from that alternativeto's list yandex because it works fine on the ipad, but it doesn't meet the direct links feature.

Greenstone.org is a digital library cms funded by the UNESCO which has a "databaseplugin" to import existing databases: http://wiki.greenstone.org/doku.php?id=en:user_advanced:using_databaseplugin
You can also export their collections to be browsed on cd/dvd