That's a good topic, routes can change everything from little events (what the protagonist does) to really big things (changing who the protagonist really is). Right now I'm not sure which routes would actually make it to my top 15 but I think it would at least include:
Rewrite Moon route - it was short but after going through all the heroines routes it felt perfect and connected everything. It also has one of my favorite VN scenes ever.
Euphoria True ending - this one was hard for me (not really into hardcore stuff) but god it was satisfying, the music for this ending was a masterpiece and it actually made me cry.
F/SN HF route - this route made me respect Shiro and I consider him one of my favorite MCs.
YMK Aeka/Nekoko - I loved Aeka's route but the best ending for me was Nekoko's.
Gotta agree with you on that one, the true end was simply brilliant.