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I'd say bookmarks (and highlights) key features for serious reading software.
Search can be hard to implement well and can be really horrible if implemented badly!
If you implement search without consideration of bookmarks (highlights and possibly text annotations) - would this be frustrating (I for one would also want the ability to search my own typed notes and bookmarks as I make quite a few).
My vote would be for some software (PDF, MobiPocket or other) with a full feature set of scribble annotation, bookmarks, highlights and text annotation (all of which could be independantly searched eventually).
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