• Hebrew edition (with dictionary link and other useful tools)
• Tanach with Mikraot Gedolot
• Parallel Hebrew and English Tanach
• Judaica Press Complete Tanakh with Rashi (in English)
• Rashi
• Ramban
• Sforno
• Rashbam (first version)
• Rashbam (second version)
• Yaakov ben ha-Rosh
• Kitzur Alshich
• Chizkuni
• Rav David Tzvi Hoffman
  • Bereishit
  • Devarim
• Ketav v’Kabbalah
  • Bereishit & Shemot
  • VaYikra & Bamidbar
  • Devarim
• Vilna Gaon
• Nechama Lebowitz – Gilyonot

Midrash

• Midrash Rabbah (at Daat.ac.il)
• Midrash Rabbah (at Tsel.org)
• Tanchuma (at Daat.ac.il)
• Mechilta (at Daat.ac.il)
• Mechilta (at Biu.ac.il)
• Sifra
• Sifrei
• Psikta D’Rav Kahana
• Tana D’Bei Eliyahu
• Yalkut Shimoni

Mishnah & Tosefta

• Mishnah
• Tosefta

Gemara

• E-Daf
• Talmud Bavli
• Talmud Yerushalmi
• Soncino Babylonian Talmud (English Translation)

Halacha

• Rambam’s Mishneh Torah
  • Hebrew Edition
  • English Edition
  • Another Hebrew Edition
  • First 7 books vocalized
• Tur
• Shulchan Aruch
• Mishna Berurah
• Aruch HaShulchan
• Halachipedia

Jewish Thought

• Kuzari
  • Hebrew version
  • English version
• Moreh Nevuchim (The Guide for the Perplexed)
  • Hebrew Edition
  • Kapach translation
  • English
• Mesillat Yesharim
  • Hebrew edition
  • English edition
• Tanya
  • Hebrew edition
  • English edition

Miscellaneous

• HebrewBooks.org (11,000 classical Hebrew books free download)
• SeforimOnline.org (Database of many scanned public domain Jewish texts)
• Gematria

Research Tools 
Online Dictionaries

• English-Hebrew / Hebrew-English Online Dictionaries
  • www.milon.co.il
  • http://milon.morfix.co.il
• Jastrow Dictionary
• Otzar Roshei Tevot
• Dictionary of Talmudic Terminology

Online Torah Texts

• WikiText Hebrew (many online Hebrew texts)
• Eparsha (Josh Cypess’ round-up of online Torah resources)

Machon Mamre Tools

• MTR Torah Freeware
  Bible, Targum Onkelos, Mishnah, Tosefta, Yerushalmi and Bavli, and Mishneh Torah in Hebrew with search engine with Hebrew interface or optional English interface
• Macon Mamre Search of Tanakh or Mishneh Torah
  

Tanakh Research Tools

• Biblical Genealogy Charts
• Bible Text Search Tools (English)
• ORT Navigating the Bible
  Torah in Hebrew, translation, transliteration and chanting

Resources for Learning Online

• Skype – can be used for 1-on-1 video calls with Chavruta(study-partner)
• Google Docs – tool for Chavruta study (use with Skype)
• Personal World Clock – check local times for your Chavruta in another time zone
• Hebrew Date Converter