My top 3 from the top of my head in no specific order would be :

1. Onani Master Kurosawa - Its really an amazing read, had me looking for the extra ending and just wow!!! Don't know why its marked as ecchi though?

2. Kimi No Iru Machi - For the same reason as Lyrad posted but i was reading harems like To Love Ru where the MC never seems to actually date the women so. . . rabblerabblerabble

3. Iris Zero & 11 eyes - put 2 just cuz i can haha these stories are about 2 guys who are outcast and feel inferior because the don't have powers or so