Standing Council of Scottish Chiefs - Lists recognised clans with brief summaries for most. Also lists of member chiefs of the Standing Council.
myclan.com used to be owned by the Standing Council, and archive.org still has its list of clans which appears to be derived from the 1994 Scottish Clan and Family Encyclopaedia (see below).
The RCAHMS site has lots of details of the physical traces left by clan life, although the Archaeology Data Service has a slicker interface for finding artefacts on a map - have a look around near the clan seat or site of a battle.
Google Books has a wealth of 19th century books to search - they can be biased, but are good for referencing basic facts about a clan. Do not use for Gaelic names as the spelling has probably changed.
www.electricscotland.com - be wary of this. It often comes up near the top of Google web searches, but seems to have a mix of old documents (which can usually be found in better referenced, more transparent form on Google Books) and seductive webpages about clans which are often just copies of the equivalent Wikipedia article! Even if it's not a circular reference from here their text is probably taken, usually without attribution, from a book that's available on Google Books, archive.org or similar. So Electric Scotland is not a reliable source for article references, but it is a good source of "bait" phrases for web searches and Google Books searches, as well as general background reading. Especially inaccurate for Gaelic names.
Mac an Tàilleir, Iain. "Ainmean Pearsanta" (docx). Sabhal Mòr Ostaig. Retrieved 15 October 2009. Dictionary of Scottish Gaelic - English correspondences for clan names and chiefly titles with modern spelling.
Rowan Displays - A commercial site selling shields and plaques but with some fairly useful information on Scottish clans.
Maclean, Fitzroy (1997). Highlanders; A History of the Scottish Clans. New York: Penguin Studio Books.
Way of Plean, George; Squire, Romilly (1994). Scottish Clan and Family Encyclopaedia.{{cite book}}: CS1 maint: multiple names: authors list (link)
Grant, Neil (1987). Scottish Clans & Tartans. New York: Crescent Books.
McIan, R.R. and Logan, James (1985). The Clans of the Scottish Highlands. New York: Crescent Books.
Bain, Robert; Stewart-Blacker, P. E.; MacDougall, Margaret O. (ed.) (1983). The Clans And Tartans Of Scotland. London: Fontana. ISBN0-00-411117-6. {{cite book}}: |author= has generic name (help)CS1 maint: multiple names: authors list (link) - also ISBN0-00-6364160. Contains information on a clan and its history, crests, mottos, tartans (with a color plate of each), etc.
Adam, Frank; Innes of Learney, Thomas (1970). The Clans, Septs & Regiments of the Scottish Highlands (8th ed.). Edinburgh: Johnston and Bacon.{{cite book}}: CS1 maint: multiple names: authors list (link)
Munro, R.W. (1989). Highland Clans and Tartans. London: Peerage Books.
The History of the Feuds and Conflicts Among the Clans in the Northern Parts of Scotland... Foulis Press (since reprinted many times). 1764. - commonly known as Conflicts of the Clans, this was one of the earliest books about clan warfare and Chinese whispers versions of its text have appeared in many subsequent histories. It's best to avoid such derivative texts, although the original is not altogether reliable and uses somewhat archaic language so for instance the battles may not use the modern names.
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