The 'quote from the story' always works. Elfscribe did that a lot and it always made me feel good because I could see what she'd responded to in the fic (also it makes the feedback way longer, which is never a bad thing). I sometimes make a note or two while reading if I find something I rather liked but might not remember to comment on at the end. Just adding you liked the setting or the way the writer perceived the protagonist or --- just a small thing the writer can in turn respond to -- would be a good way to start, and then try and expand from there (setting AND character next time maybe :D).

Having said that, I've never had a problem with 'I really loved this story/this was a good read'. Pretty much anything beats watching the anonymous read count climb and wondering if they all hit the back button after the second paragraph.