You've probably heard of Katawa Shoujo, one of the more recent examples of the genre. Juniper's Knot is another good choice, but it's a kinetic novel (no choices that affect the ending / overall narrative) so that's that. KS is highly romantic in nature, so that might not be what you want.
The Visual Novel Database (VNDB.org) is pretty much the place to research and find new visual novels. ATP Projects (atpprojects.wordpress.com) is another good place to look for story-based titles. Some are really good, some are thoughtful, and some might not be everyone's cup of tea.
Insani.org is where the altogether projects originated for the most part, and where you can find other works like True Remembrance.
Either way, finding good freeware visual novels is not a difficult task. Even the Ren'Ai archive http://www.renai.us
/ holds a few gems.