Modified gravity theories have richer observational consequences for large-scale structure than conventional dark energy models, in that different observables are not described by a single growth factor even in the linear regime. We examine the relationships between perturbations in the metric potentials, density and velocity fields, and discuss strategies for measuring them using gravitational lensing, galaxy cluster abundances, galaxy clustering/dynamics and the ISW effect. We show how a broad class of gravity theories can be tested by combining these probes. A robust way to interpret observations is by constraining two key functions: the ratio of the two metric potentials, and the ratio of the Gravitational ``constant'' in the Poisson equation to Newton's constant. We also discuss quasilinear effects that carry signatures of gravity, such as through induced three-point correlations. Clustering of dark energy can mimic features of modified gravity theories and thus confuse the search for distinct signatures of such theories. It can produce pressure perturbations and anisotropic stresses, which breaks the equality between the two metric potentials even in general relativity. With these two extra degrees of freedom, can a clustered dark energy model mimic modified gravity models in all observational tests? We show with specific examples that observational constraints on both the metric potentials and density perturbations can in principle distinguish modifications of gravity from dark energy models. We compare our result with other recent studies that have slightly different assumptions (and apparently contradictory conclusions).

19 pages, 3 figures. Submitted to PRD