We give an overview of the work done with the Laboratoire National de Métrologie et d'Essais-Systèmes de Référence Temps-Espace (LNE-SYRTE) fountain ensemble during the last five years. After a description of the clock ensemble, comprising three fountains, FO1, FO2, and FOM, and the newest developments, we review recent studies of several systematic frequency shifts. This includes the distributed cavity phase shift, which we evaluate for the FO1 and FOM fountains, applying the techniques of our recent work on FO2. We also report calculations of the microwave lensing frequency shift for the three fountains, review the status of the blackbody radiation shift, and summarize recent experimental work to control microwave leakage and spurious phase perturbations. We give current accuracy budgets. We also describe several applications in time and frequency metrology: fountain comparisons, calibrations of the international atomic time, secondary representation of the SI second based on the (87)Rb hyperfine frequency, absolute measurements of optical frequencies, tests of the T2L2 satellite laser link, and review fundamental physics applications of the LNE-SYRTE fountain ensemble. Finally, we give a summary of the tests of the PHARAO cold atom space clock performed using the FOM transportable fountain.