[Katawa Shoujo, the queen of homemade VN]

I didn't care for it much myself, but it's free and every VN fan should experience it.

[Aokana Release by Nekonyan [UPDATED]]

Really liked this one. One of the best VN's I've ever played. I came in with moderately high expectations, so I'm glad those expectations were exceeded.

Misaki's route in particular made the game great. I wasn't particularly high on the other routes for a few reasons, but I can see why some people would love Asuka's/Mashiro's routes (Rika's is lacking though). The OST was amazing, and the common route was strong too. I will remember this one fondly for a long time.

It's a great value too. $32-$35 for a single play through of around 30 hours is fantastic by today's standards. Plus the h-scene patch is free for the Steam version (some like to charge for that).