Do you use the Ao3 Review plugin? It give you a floaty comment box that follows you down the page so you can paste in lines you like. I don't usually use it on first read (who knows on first read if you are going to want to comment, or even read to the end?) but I find it very handy once I've got to the end and made the 'I must comment on this!!!' decision to goback to the the start and skip through copy-pasting good lines or just reacting to the storyline.

Not that I'm exactly a great commenter, mine tend to be a bit on the short side, but I think it does help.

On chaptered fiction, I like to respond to the characters almost as if they were telling me about what they did afterwards? That gives you comments like : OMG Fingon, what were you THINKING??? How are you going to get out of this one??? Which can be fun for the writer and I think are actually easier to reply to than pure praise.