Honestly, a lot of the most passionate Reddit recommendations come with a content warning label attached. 'Saya no Uta' is praised for its horror and philosophical story, but it's intensely disturbing. 'Katawa Shoujo', a free VN born from 4chan, gets love for its surprisingly sensitive handling of disability in a romance framework.
It really depends on what kind of story you're after. Reddit tends to separate 'nakige' (cry-inducing stories) like 'Clannad' and 'planetarian' from plot-heavy mysteries like 'Raging Loop' or the Zero Escape series. Browsing by flair on the subreddit is way more effective than asking for a blanket 'best' list.