We describe a generic framework for representing and reasoning with annotated Semantic Web data, a task becoming more important with the recent increased amount of inconsistent and non-reliable meta-data on the Web. We formalise the annotated language, the corresponding deductive system and address the query answering problem. Previous contributions on specific RDF annotation domains are encompassed by our unified reasoning formalism as we show by instantiating it on (i) temporal, (ii) fuzzy, and (iii) provenance annotations. Moreover, we provide a generic method for combining multiple annotation domains allowing to represent, e.g., temporally-annotated fuzzy RDF. Furthermore, we address the development of a query language – AnQL – that is inspired by SPARQL, including several features of SPARQL 1.1 (subqueries, aggregates, assignment, solution modifiers) along with the formal definitions of their semantics.