Andy Waddington's site is worth a visit if you're planning on building a wooden boat - he seems to produce some fascinating and elegant solutions.
Building your own folding boats - Tom Yost can teach you everything you ever wanted to know about DIY folding boats.
Bryan Hansell's site is well worth a visit for ideas and plans, and a host of other sea-kayking related things.
Chesapeake Light Craft - sell kits and designs for kayaks. Here's some great pics of the build of a Chesapeake 17. Shaman Kayaks is also well worth a look for the wonderful images of boats, paddles and other traditional goodies.
Dougs Boat Page could give you some boat-building ideas as well as designs.
Driftwood & scraps - yes, it is possible to build a kayak from the driftwood you'll find on a beach.
Fyne Boat Kits in Cumbria, UK, offer some pretty looking kayak plans & kits.
Igdlorssuit kayak - also known as the "Ken Taylor kayak", this series of articles from Bryan Hansell details the build of a cedar strip replica of the boat which spawned the Anas Acuta, arguably the father of a great many current designs. Well worth reading for generic self-build tips.
"John & BJ's Place" has a nice page on the various types of self-build boats
Laughing Loon offer plans and kits.
Mikebelluk designed and built a rather splendid boat from "21 metres of western red cedar decking". His blog documents the build.
Nick Schade's book on building strip built kayaks might be worth reading.
Outer-Island woodstrip kayak - this site offers some building tips, including a very neat method of fitting VCP type hatches to a curved deck.
Redfish have wooden kayak designs.
Ross Leidy's Kayak Building site is worthy of a visit - not content with just buying a kit and building it, this man designed his own software to design the boat - and then goes on to make his own wooden "J" cradles, paddle and a fibreglass seat.
Selway Fisher in Wiltshire, UK, offer a range of DIY designs. Their links page provides a massive range of self-build related links.
Shrike - a lightweight sea kayak for home constuction." As of end July 2014, 454 copies of the plans downloaded to 34 different countries, with construction underway from Estonia to Dubai to Florida to Canada and even Portsmouth".
Skin-on-frame - building a traditional kayak - a fantastic picture set. Want to build one? Anders Thygesen is your man, although you'll need to go to Norway. Sue Ellcome did - she built a beautiful sof boat. This article on Wolfgang Brinck's site also contains superb pictures and outlines the build process.
Three-part (or two-part) kayaks - "Ceegee" modified a standard Rockpool to make a three-part version - a truly amazing job. These three posts detail the work involved - Initial thoughts - Part 1 and Part 2 of the job.
Tom's Guillemot is truly a wonderous thing of beauty.
Traditional boats, techniques and paddle designs can all be found on Qujaq USA's great site.
WaveLength, an excellent Canadian magazine with an on-line version, is worth checking for articles and advertisers working in the self-build area.