Protagonist + childhood friend would be the obvious answer, but more rare is when they end with their or someone else parent (I think you hinted that).
Unexpected couple?
Is this bait for things like Onodera's fans being upset with the ending?
or are you looking for a list of manga where the poster cover girl didn't win?
like Ookami Shounen? or KamiNomi?
Unexpected like School Rumble's Harima Kenji epilogue?
Another couple I didn't expect end up together was Hirunaka Ryuusei,
a couple that I genuinely think the author didn't originally plan to end up like this is that OtakuxGal POV story