Marginalia Weblog - Viktor Lofgren's Weblog, mainly regarding development and web search
Garrit Franke He's knowledgeable and funny. No need for more, tech-related
Seirdy - Privacy, security, software... all the stuff I used to read on the old internet... back on the old internet
Low-tech magazine Interesting uses for some not so high tech. Sort of a personal rebellion against (high)tech-centric world. Run on solar-powered computer somewhere in Spain
KevQuirk - Personal blog of Infosec specialist, he's got some great essays and some very neat projects (like simple.css and 512kb.club of which I'm now a proud member)
Search
Marginalia Search - Viktor Lofgren's Open Source search engine targeting small and indie webspace
Greppr - Interesting small experiment. Surprisingly working for being so small :-)
Mojeek - Probably the biggest European search engine, one of the biggest search engines in the world and definitely the biggest independent one.
Directories
Indieseek - Directory of small and independent sites