We present the results of a program to acquire high-quality optical spectra of X-ray sources detected in the ExtendedChandra Deep Field-South (E-CDF-S) and its central 2 Ms area. New spectroscopic redshifts, up to z = 4, are measured for 283 counterparts to Chandra sources with deep exposures (t ∼ 2-9 hr per pointing) using multi-slit facilities on both VLT (VIMOS) and Keck (DEIMOS), thus bringing the total number of spectroscopically identified X-ray sources to over 500 in this survey field. Since our new spectroscopic identifications are mainly associated with X-ray sources in the shallower 250 ks coverage, we provide a comprehensive catalog of X-ray sources detected in the E-CDF-S including the optical and near-infrared counterparts, determined by a likelihood routine, and redshifts (both spectroscopic and photometric), that incorporate published spectroscopic catalogs, thus resulting in a final sample with a high fraction (80%) of X-ray sources having secure identifications. We demonstrate the remarkable coverage of the luminosity-redshift plane now accessible from our data while emphasizing the detection of active galactic nuclei (AGNs) that contribute to the faint end of the luminosity function (L 0.5-8 keV ∼ 10 43 -10 44 erg s −1 ) at 1.5 z 3 including those with and without broad emission lines. Our redshift catalog includes 17 type-2 QSOs at 1 z 3.5 that significantly increases such samples (2×). Based on our deepest (9 hr) VLT/VIMOS observation, we identify "elusive" optically faint galaxies (R mag ∼ 25) at z ∼ 2-3 based upon the detection of interstellar absorption lines (e.g., O ii+Si iv, C ii], C iv); we highlight one such case, an absorption-line galaxy at z = 3.208 having no obvious signs of an AGN in its optical spectrum. In addition, we determine accurate distances to eight galaxy groups with extended X-ray emission detected both by Chandra and XMM-Newton. Finally, we measure the physical extent of known large-scale structures (z ∼ 0.7) evident in the CDF-S. While a thick sheet (a radial size of 67.7 Mpc) at z ∼ 0.67 extends over the full field, the z ∼ 0.73 structure is thin (18.8 Mpc) and filamentary as traced by both AGNs and galaxy groups. In the Appendix, we provide spectroscopic redshifts for 49 counterparts to fainter X-ray sources detected only in the 1 and 2 Ms catalogs, and 48 Very Large Array radio sources not detected in X-rays.