Sanskrit / Devanagari:

Sanskrit Reader Companion. A free tool developed by Gérard Huet that magnificently deconstructs Sanskrit and shows multiple translation variations, including the original root and how it was declined.
http://sanskrit.inria.fr/DICO/reader.en.html (for abbreviations used, click here)
There are various other tools available, such as verb conjugation and noun declension, and a searchable digital format of the Monier-Williams dictionary.

IAST -> Devanagari -> IAST converter: (excelent tool)
http://epandit.shrish.in/tools/IAST-DV-IAST/ (archived)

Excellent grammar guide for beginners in learning Sanskrit. I have learned a great deal.
http://www.learnsanskrit.org/grammar

If you want to learn Sanskrit, have a look at the following excellent page:
https://www.sanskrit-trikashaivism.com/en/sanskrit/101

Tool to convert files encoded in various character sets to utf-8
http://www.innovatrix.co.in/unicode/fileconverterindex.php5

Text & Resources:

Sacred-Texts: Huge depot of converted free e-books; mostly from the public domain:
http://www.sacred-texts.com/

Charitable programs:

Behind Every Temple is a Non-Profit Organization with a mission to support, protect and promote Sanatana Dharma
https://behindeverytemple.org

Arsha Seva Kendram is a non-profit organization founded to impart the teaching and attitude of Seva.
https://www.arshasevakendram.org/

Hinduism

Lots of scriptures such as the Puranas, Vedas, Sutras and many other interesting texts. All of them are in PDF or HTML format.
http://www.indianscriptures.com/scriptures

The Bhagavad Gita with english grammar syntax and different commentaries in sanskrit. The grammar syntax is very thorough.
http://www.bhagavadgita.eu/en/

Excellent site with an English translation of the Bhagavad Gita including various commentaries (also translated)
http://www.bhagavad-gita.us/

The Bhagavad Gita with 4 different commentaries, transliteration and audio for every verse.
http://www.bhagavad-gita.org/Gita/intro.html

The full Śrīmad Bhāgavatam. Transliteration and Commentary for every verse.
http://srimadbhagavatam.com/en

Plenty of free articles and books. Also supports charity projects.
http://www.astrojyoti.com/

Hinduism / blogs:

ManBlunder: Various articles and books with excellent commentaries free of charge.
http://www.manblunderplus.com/
(old) http://www.manblunder.com/

Very good up-to-date blog with various articles on India and Hinduism. Everything is well-documented with sources.
https://ramanan50.wordpress.com/

Buddhism:

84000: A noble cause that aims to translate the words of the Buddha.
http://84000.co/

Abhidhamma: Lots of books and information; mainly Buddhism:
http://www.abhidhamma.com/

Very pleasant wiki-like Buddhism-resource center:
http://www.dhammawiki.com/

Probably the best discussion forum for all your buddhism questions and answers:
http://www.dhammawheel.com/index.php

Access to Insight: One of the best concerning Theravāda Buddhism:
http://www.accesstoinsight.org/

City of 10,000 Buddhas: Information and Text regarding Tripitaka Master Hsuan Hua
http://www.cttbusa.org/

Tibetan:

Large wiki-like site with many entries
http://www.rigpawiki.org/

Rangjung Yeshe Wiki: Online Tibetan-English Dictionary with nearly 200,000 entries!
http://rywiki.tsadra.org/index.php/Main_Page

ACIP: Asian Classics Inout Project. Excellent project that travels around the world to save fragile texts from extinction
http://www.asianclassics.org

Database of high-res images of Tibetan artworks. Staggering amount and incredible detail.
http://www.himalayanart.org/