Mishna Yomi
Daily learning of Mishna (2 a day), in text and shockwave audio
http://www.shemayisrael.co.il/mishna/index.htm

The Structured Mishnah
"Hamishnah C'Darcah" is a new color-coded structured edition of the Mishnah. The full text appears on the site as well as articles on the structure of the Torah and the Mishnah.
http://chaver.com/

A Page of Talmud
Description and explanation of the layout of a traditional page of the Talmud.
http://www.ucalgary.ca/~elsegal/TalmudPage.html

E-daf.com
Online copy of original Talmud (in Gif format), page by page.
http://www.e-daf.com

Master Daf - Listen and Learn the Talmud
Series of lessons on the entire Babylonian Talmud by R. Avraham Kosman. Every word of the Talmud is read in its original, translated into English, and explained according to the basic meaning of the text. Paid subscription service.
http://www.masterdaf.com

Kolell Dirshu International, Cleveland Branch
Contains MP3 audio of daily Gemorah learning and information about the program.
http://www.dirshucleveland.com

Daf Yomi with Rashi Embedded,
The Gemara Daf-Yomi with embedded Rashi, paragraphed and punctuated. All of Seder Nashim, Baba Kama, Baba Metsia, Baba Basra to current Daf, Taanith and Rosh Hashana.
http://www.geocities.com/yeshol/

Online Talmud Study With Text and Audio
Streaming audio Talmud classes with simultaneous text, from California Chabad.
http://www.beverlyhillschabad.com/gemara.htm

Dafyomi Advancement Forum
Comprehensive site dedicated to supplying free, multi-level study material and lists of resources for those studying Talmud according to the 7-year Dafyomi cycle.
http://www.dafyomi.co.il/

Chavruta - online Talmud commentary
Online edition of the 60 vol. series on the Talmud - Chavruta. Presented in Hebrew and English.
http://chavruta.torah.net/english.php

Virtual Jerusalem - Daf Yomi
Updated weekly daf yomi commentary.
http://www.virtualjerusalem.com/judaism/judaism.php?sid=59

Introduction to the Talmud
Lessons on the beginning of tractate Brachot.
http://yeshiva.faithweb.com

Daily Gemara Shiur
Comprehensive daily audio lessons on the Daf Yomi by R. Eli Mansour. Includes an image of the daily daf and podcast options.
http://www.dailygemara.com/

Daf Yomi Lessons
Free archive of audio lessons on the complete Talmud by R. Grossman. Contains separate lessons for Mishnayot.
http://www.dafyomi.org/

Yerushalmi Online
Resources on the Daf Yomi of the Jerusalem Talmud, featuring audio lessons, articles and books (both free in PDF, and commercial).
http://www.yerushalmionline.org/