While there are few websites that make available inscriptions from Israel/Palestine during the Persian, Hellenistic, and Roman periods, the WWW does contain many resources for study of the epigraphy, archaeology and history of Israel/Palestine, the Near East, and the classical world.
The West Semitic Research Project: Housed at USC, an image collection that includes a wide variety of inscriptional material, particularly in the languages and scripts of Northwest Semitic.
InscriptiFact: A database of high-resolution images of ancient Near Eastern inscriptions and papyri. The focus of the database is on artifacts that pre-date the Persian period.
The Northwest Semitic Archive: Containing inscriptions in Ammonite, Aramaic, Edomite, Hebrew, Moabite, Philistine, Phoenician, Proto-Cannanite, and Proto-Sinaitic. The inscriptions are transcribed into Latin characters, and the searching can be somewhat cumbersome.
The Ancient Hebrew Research Center's Ancient Semitic Inscriptions site contains a number of beautiful pictures of ancient Semitic inscriptions, and is useful for seeing and charting different Semitic scripts.
The Electronic Text Corpus of Sumerian Literature is a well-designed site that provides both searchable transcriptions and translations of many Sumerian documents.
K.C. Hanson’s Collection of Ancient Documents: A useful collection of inscriptions and documents relating to the study of early Judaism and Christianity. For most entries he includes not only basic information about the object, but also a transcription (for Semitic languages in transliteration), English translation, bibliography, and interesting set of discussion questions. Among some of the more interesting texts relating to this project are the Yavneh-Yam Ostracon, the Gezer Calendar), an inscription forbidding foreigners to enter into the Second Temple, the Theodotus inscription (the earliest synagogue inscription from Israel/Palestine), and an inscribed ossuary that may mention the high priest Caiphas.
The Epigraphische Datenbank Heidelberg: Probably the most extensive collection of Greek and Latin epigraphy. Contains several Latin inscriptions from Israel/Palestine.
Inscriptions of Aphrodisias: An edition of the online corpus of the Greek inscriptions of Aphrodisias, a city in Asia Minor. This is the most polished project to date to use the EpiDoc electronic editorial conventions (see below).
The Corpus Inscriptionum Latinarum: Contains texts (many drawn from the Epigraphische Datenbank Heidelberg) of some of the CIL II volumes, along with photographs.
The Centre for the Study of Ancient Documents at Oxford: Maintains many images of Greek and Latin inscriptions.
The US Epigraphy Project: A large and growing guide to Greek and Latin inscriptions now located in the US.
Among the online tools available for the study of inscriptions is a list of Greek Abbreviations and Letter Combinations (Ligatures) commonly used in inscriptions, scanned from Bernhard Abraham van Groningen, Short Manual of Greek Palaeography, (Leiden: 1940).
As part of their work on the Diccionario Griego-Español (DGE), a new Greek-Spanish dictionary, scholars have developed and made available a Concordance of Greek Inscriptions that correlates the different editions of inscriptions that have been published multiple times.
Website Attica at the University of Toronto: Contains a database of the names found in Athenian inscriptions. The Lexicon of Greek Personal Names is even more ambitious, seeking 'to collect and publish all ancient Greek personal names, drawing on the full range of written sources from the 8th century B.C. down to the late Roman Empire.'
The Comprehensive Aramaic Lexicon Project at the Hebrew Union College/Jewish Institute of Religion is a growing database of Aramaic texts from antiquity through the Middle Ages.
Pleiades is a site devoted to mapping the ancient world.
Suda On Line: A Greek lexicographical reference work from the Byzantine period.
Abbreviations in Latin Inscriptions: Tom Elliot has done an admirable job of assembling a bewildering array of abbreviations.
The Prosopographia Imperii Romani: In German, is a handy database of Latin names.
EpiDoc: A collaborative effort to create flexible standards for the digital encoding and interchange of scholarly and educational editions of ancient texts.
The Stoa Consortium: Contains collections of resources, as well as maintaining a blog.
Inscriptions can best be understood in their local, archaeological contexts. For a quick guide to the state of archaeological excavations in particular sites in Israel, Archaeological Sites in Israel is quite useful. Compiled by the Israeli government, it links to brief descriptions of past and current archaeological work at each site.
Several other sites have educational value. The International Catacomb Society focuses on research on the Roman catacombs, with particular interest in Jewish catacombs. The site contains a number of good maps of these catacombs as well as images and bibliographies available to members. An online exhibit, Scrolls from the Dead Sea, offers a useful introduction to the community at Qumran. The Virtual World Project is an innovative attempt to make accessible archaeological plans and multimedia presentations of sites in the ancient Mediterranean.
The Israeli Antiquities Authority runs a very informative and sophisticated educational site, the Jerusalem Archaeological Park, devoted to the archaeology of Jerusalem from its origins to the beginning of the twentieth century.
In addition to archaeology, both contemporary literature and history are contexts for the study of these inscriptions. Standard printed versions of the Bible, Mishnah, Palestinian and Babylonian Talmuds can be found in a Hebrew website http://kodesh.snunit.k12.il. Links to many other texts (and other resources), both in the original and translation, can be found through the resource site of the Dinur Center for the Research of Jewish History.
There are a vast number of sites devoted to Greek and Latin archaeology and literature online. Probably the most extensive of these is the Perseus Digital Library. Metis provides access to many plans of and articles on archaeological excavations.