I use a highly durable method: pen and paper. I keep a folded sheet of paper and ballpen with my ebook reader, and for every book I read I note whatever looks weird to me (unknown words, OCR errors, wrong punctuation, missing formatting). Every few days I bring the paper to the computer and do what's needed: if it's a book I have created, I make the corrections; if it's a book created by someone else, I add the corrections to a text file, which I sent to the creator when the book is finished (in every case, I try to compare with scans of printed editions available online). Once the paper is full (which takes some time, because my writing is rather small, and I can be very succint), I just throw it away.
But I would like a reader with some annotation support.
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