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 searchable digital edition of the Monier-Williams dictionary and various other Sanskrit compendiums.
http://www.sanskritdictionary.com/
For quick search of a word, just append ?q=### after the URL.

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 excelent page:
https://www.sanskrit-trikashaivism.com/en/sanskrit/101

How to pronounce IAST (International Alphabet of Sanskrit Transliteration)
http://www.theosociety.org/pasadena/sk-pron/skpro-hp.htm

Very usefull Sanskrit-English (or the other way around) with a massive database, that gives the definition of a word and the Sanskrit text with actual sanskrit characters. Keep this close if you are reading books about Hinduism for example.
http://spokensanskrit.de/

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

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/

Text & Recourses:

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

Project Gutenberg: Lots of free e-books; various subjects; many of them are proofread.
http://www.gutenberg.org

HolyBooks.com: Regularely updaed e-books for free download.
http://www.holybooks.com/

Religion Information:

Compare different sets of Religion:
http://www.diffen.com/difference/Category:Religion

Philosophy:

Internet Encyclopedia of Philosophy: Several well-written articles.
http://www.iep.utm.edu/

Other:

Kashmir Lounge:
http://www.kashmirlounge.com | The best lounge in Amsterdam offering relaxation in an Indian environment. Don't miss out on this place when you visit Amsterdam (in the Netherlands)

Free fonts for lots of Languages and dialects such as Devanagari, Arabic, Hebrew and Korean just to name a few. Usefull when doing research in ancient history.
http://www.omniglot.com/links/fonts.htm