Electronic transport properties of single-molecule junctions have been widely measured by several techniques, including mechanically controllable break junctions, electromigration break junctions, and by means of scanning tunneling microscopes. In parallel, many theoretical tools have been developed and refined for describing such transport properties and for obtaining numerical predictions. Most prominent among these theoretical tools are those based upon density functional theory. In this review, theory and experiment are critically compared, and this confrontation leads to several important conclusions. The theoretically predicted trends nowadays reproduce the experimental findings well for series of molecules with a single well-defined control parameter, such as the length of the molecules. The quantitative agreement between theory and experiment usually is less convincing, however. Two main sources for the quantitative discrepancies can be identified. Experimentally, the atomic structure of the junction typically realized in the measurement is not well known, so simulations rely on plausible scenarios. In theory, correlation effects can be included only in approximations that are difficult to control for experimentally relevant situations. Therefore, one typically expects qualitative agreement with present modeling tools; in exceptional cases a quantitative agreement has already been achieved. For further progress, benchmark systems are required that are sufficiently well defined by experiment to allow quantitative testing of the approximation schemes underlying the theoretical modeling. Several key experiments can be identified suggesting that the present description may even be qualitatively incomplete in some cases. Such key experimental observations and their current models are also discussed here, leading to several suggestions for extensions of the models toward including dynamic image charges, electron correlations, and polaron formation.