This is not meant to be comprehensive, but contains a number of sites and links that might be of interest to those interested in working on digital humanities projects relating to Jews and Judaism in (particularly late) antiquity. I am happy to add and correct this list, so please feel free to send me your suggestions. Over time, I may well annotate it as well.
Sites Dealing Directly with Jews and Judaism in Late Antiquity
Accordance ($)
Bar-Ilan Responsa Project ($)
BibleWorks ($)
Corpus Tannaiticum: http://mishna.huma-num.fr/
Digital Mishnah: https://www.digitalmishnah.org/
Hachi Garsinan: https://fjms.genizah.org/
Judaism and Rome: http://judaism-and-rome.cnrs.fr/
Mechon Mamre: https://www.mechon-mamre.org/
Sefaria: https://www.sefaria.org/texts
THALES Lectionary Project: http://www.lectionary.eu/
Torat Ha-Tannaim: https://www.biu.ac.il/JS/tannaim/
Tosefta Online: http://www.toseftaonline.org/
Yerushalmi Online: http://www.yerushalmionline.org/
Inscriptions of Israel/Palestine: http://www.brown.edu/iip
Israel Antiquities Authority (National Treasures Online): http://www.antiquities.org.il/t/PeriodsList_en.aspx
Levantine Ceramics Project: https://www.levantineceramics.org/
Sites with Data Relating to the Study of Jews and Judaism in Late Antiquity
American Numismatic Society: http://numismatics.org/search/
Catacomb Society (some images): http://www.catacombsociety.org
CIL: https://arachne.uni-koeln.de/drupal/?q=en%2Fnode%2F29
Corpus Scriptorium: http://copticscriptorium.org/
Digital Latin Library: https://digitallatin.org/
Epigraphic Database Heidelberg: https://edh-www.adw.uni-heidelberg.de/home
Epigraphic Database Bari: http://www.edb.uniba.it/
Open Greek and Latin Project: https://www.dh.uni-leipzig.de/wo/projects/open-greek-and-latin-project/
Papyri.info: http://papyri.info/
Perseus Digital Library: http://www.perseus.tufts.edu/hopper/
Syriaca.org: http://syriaca.org/
Thesaurus Linguae Graecae ($): http://stephanus.tlg.uci.edu/
Lexica, etc.
Comprehensive Aramaic Lexicon: http://cal.huc.edu/
Lidell Scott Online: http://www.perseus.tufts.edu/hopper/resolveform?redirect=true
Jastrow Online: http://www.dukhrana.com/lexicon/Jastrow/
Ma’agarim: http://maagarim.hebrew-academy.org.il/Pages/PMain.aspx
Rabbis of Antiquity (alphabetized spreadsheet, beta): http://mlsatlow.com/2017/08/08/naming-rabbis-a-digital-list/
Rav Milim: https://www.ravmilim.co.il/naerr.asp
Standards
Epidoc: https://sourceforge.net/p/epidoc/wiki/Home/
Getty Art and Architecture Thesaurus: http://www.getty.edu/research/tools/vocabularies/aat/
GODOT (date reconciliation): https://godot.date/about
Period.O (periodization): http://perio.do/en/
Pleiades (geographical): https://pleiades.stoa.org/
Text Encoding Initiative (TEI): http://www.tei-c.org/
Virtual International Authority File: https://viaf.org/
Tools
Classical Language Toolkit: http://cltk.org/
Dicta: http://dicta.org.il/
GEPHI (network analysis): https://gephi.org/
Hebrew Parser: http://onlp.openu.org.il/
MALLETT (Topic Modeling): http://mallet.cs.umass.edu/topics.php
VOS Viewer: http://www.vosviewer.com/
Voyant: https://voyant-tools.org/
Synthetic Projects
These do not deal with antiquity, but I include them here because they are interesting models for digital humanities projects that might be applied to data from antiquity.
Cambridge Group for the History of Population and Social Structure: https://www.campop.geog.cam.ac.uk/
Footprints: https://footprints.ccnmtl.columbia.edu/
Mining the Dispatch: http://dsl.richmond.edu/dispatch/Topics
ORBIS: http://orbis.stanford.edu
Republic of Letters: http://republicofletters.stanford.edu
Six Degrees of Francis Bacon: http://www.sixdegreesoffrancisbacon.com/