Spoiler Alert, click show to read:
Digital Libraries
http://www.jstor.org/ Probably the best online, with a gigantic selection of papers. Most cost money, but there are a very small amount for free.
http://www.academia.edu/ Much smaller selection than JSTOR, but all are free (I'm pretty sure).
http://www.scribd.com/ You'd be lucky to find a paper or book you're looking for on here, but everything's free.
http://www.perseus.tufts.edu/hopper/collection?collection=Perseus%3Acollection%3AGreco-Roman Another great site with lots of great info.
Historia
General
http://en.wikipedia.org/ Sometimes reliable, sometimes not. Depends on how subjective the topic is. Sometimes the articles are very professional.
http://scholar.google.com.au/ The best way to search for articles, journals and such.
http://www.karwansaraypublishers.com/cms/karwansaray/ancient-warfare.html Publishers of the Ancient Warfare magazine, they also publish online articles; rather short, but worth a mention.
Rome & Italics
http://www.roman-empire.net/ A nice introductory website to Roman history.
http://romanarmy.info/site_map.html A highly accredited site for Roman warfare and tactics.
http://members.tripod.com/~S_van_Dorst/index.html "Sander's Homepage", contains lots of information on all eras of the Roman army.
http://www.roman-britain.org/military/british_cohortes.htm a book detailing the Imperial Roman Auxilia units.
http://www.sanniti.info/indexen.html lots of info on the Samnites.
http://michael-engel.io.ua/album505865_0 "The Cultural and Military Significance of the South Italic Warrior's Panoply from the 5th to the 3rd Centuries BC" by Michael Burns.
http://www.digressus.org/articles/romanizationpp060-085-burns.pdf "The Homogenisation of Military Equipment Under the Roman Republic" by Michael Burns.
https://archive.org/stream/auxiliaofromanim00cheerich#page/n5/mode/2up "The Auxilia of the Roman Imperial Army" by G. L. Cheesman
Hellenes
http://members.tripod.com/~S_van_Dorst/Alexander.html the army of Alexander the Great.
http://www.larp.com/hoplite/index.html Greek Hoplite website.
Celts
http://www4.uwm.edu/celtic/ekeltoi/ a great site containing high quality studies on all areas of the Celts and Celtiberians
Persians & Iranians
http://www.iranicaonline.org/ "The Encyclopędia Iranica is a comprehensive research tool dedicated to the study of Iranian civilization in the Middle East, the Caucasus, Central Asia, and the Indian subcontinent."
http://www.cais-soas.com/index.htm "The First and Most Comprehensive, Informative and Scholarly Website Dedicated to Ancient Iran and Iranian Civilization."
Naval
http://www.triremetrust.org.uk/tt-thesis.htm a study titled, "The trierarchy, its place in Athenian society, and how much did a trieres cost?"
Maps
http://empiresinhistory.com/ An interactive map of the Roman Empire, from it's traditional founding to 400 AD
http://www.euratlas.com/index.html "Euratlas is a website dedicated mainly to the historical geography of Europe but it offers also a world atlas and a wide collection of pictures in order to give a comprehensive view of history and geography."
http://www.hipkiss.org/cgi-bin/maps.pl?book=J+M+Dent+And+Sons+-+Atlas+Of+Ancient+And+Classical+Geography scans of old, but very high quality, geopolitical maps of the ancient world.
Authors of Antiquity
http://penelope.uchicago.edu/Thayer/E/Roman/home.html Contains many maps and photos of Roman towns and monuments, and also provides over 50 translations of works and authors from antiquity
http://www.perseus.tufts.edu/hopper/collection?collection=Perseus%3Acollection%3AGreco-Roman Can find most ancient texts on this site, like Livy's surviving work and Xenophon's Anabasis. There's many, many more.
Linguistics
http://www.wiktionary.org/ A great linguistic dictionary.
http://www.utexas.edu/cola/centers/lrc/ielex/ Plenty of great info on IE languages, and also contains an IE lexicon.
http://starling.rinet.ru/cgi-bin/query.cgi?basename=\data\ie\piet&root=config&morpho=0 For IE etymology.
http://spokensanskrit.de/index.php?script=HK&beginning=0 Sanskrit dictionary, a lovely language that's considered very conservative from original IE.
http://indo-european.info/dictionary-translator/translate/English/Indo-European/ A PIE Dictionary/Lexicon
http://www.palaeolexicon.com/ "Palaeolexicon is a tool for the study of ancient languages."
http://www.lexilogos.com/english/greek_ancient_dictionary.htm an ancient Greek dictionary
http://s_van_dorst.tripod.com/Ancient_Warfare/Greece/greek_glossary.html ancient Greek military terms
http://members.tripod.com/~S_van_Dorst/glossary.html ancient Roman military terms
http://dnghu.org/indoeuropean/indo-european.htm A great, but outdated, book on Indo-European grammar
http://www.wales.ac.uk/en/CentreforAdvancedWelshCelticStudies/ResearchProjects/CompletedProjects/TheCelticLanguagesandCulturalIdentity/CelticLexicon.aspx free to download either Proto-Celtic > English, or English > Proto-Celtic lexicons
http://phoenicia.org/phoeniciandictionary.html online English to Phoenician dictionary
http://www.arbre-celtique.com/encyclopedie/mots-et-etymons-de-la-langue-gauloise-4.htm Celtic (or perhaps more specifically Gaulish) lexicon/dictionary (in French)
http://oda.perso.worldonline.fr/dicogaulois.htm another Gaulish lexicon in French (English version seems to be down)
https://archive.org/details/DictionaryOfMMP Dictionary Of Manichean Middle Persian & Parthian (great stuff)
http://etruscans1.tripod.com/Language/ an Etruscan dictionary
http://users.cwnet.com/millenia/ETRUSCANDICTIONARY.htm another Etruscan dictionary that attempts to express the relation between Finno-Urgic languages
http://member.melbpc.org.au/~tmajlath/etruscan.html and another study on Etruscan language that explores its similarities with Finno-Urgic languages.