Because the original topic hasn't been updated in three years, I decided to re-make the whole thread, add some new links and polish or throw out the old ones. As an homage to the original thread:
Tails_155 wrote:This was an Idea for how to make a site referencing various educational links on topics, I may or may not make a site this summer, granted time. Any other recommended links will be added 
I have a plot so far:
Philosophy - GeneralEbonMusings............... - TheologyJesus Never ExistedDaylight AtheismRichard Dawkins' Official SiteThe Atheist NexusWhy Won't God Heal Amputees?BibleGod aka Skeptics annotated BibleEvil BibleThe Vatican's BillionsThe God Delusion, Bible, Qu'Ran, Bagavad Gita, etc.
Science - CombinedMade Easy seriesThe Discover Magazine BlogsScale of the UniverseRichard Harter's Website (RIP)ScienceFridayNeuroskeptic BlogIdeonexusSenseAboutScience...........- Open Access JournalsA list of bad JournalsPLoS...........- Earth Science - General.................................- GeographyGapminderWorldmeterWorldmapper.................................- BiologyThe Eyes of Nye: Race -
1,
2,
3Darwin 2009Panda's Thumb - news on evolution topics
LocoLobo - AronRa's "Homepage" on YouTube
Sean Carroll's column "Remarkable Creatures"The Fossil SongInsect PhotographyWikimedia - SpeciesHumanorigins - From the Smithsonian Institute
Genome.gov - Technical terms in biology explained - Biological Dictionary
DevonianTimes <- A page about Tiktaalik
Tiktaalik <- Guess what...?
WTF Evolution? Ever wanted really dumb "design"? Here's a whole page of it.
EvolutionaryModel - Need Info about ERV's, Vestigialities, etc.? Here you go!
...........- AstronomyInternational Year of Astronomy 2009Bad AstronomyNASA - Astronomy Picture of the Day...........- Physics - GeneralKhan Academy's Physics VideosHyperphysics - Explaining everything about physics you'll need in your daily life... and more!
........................- Mechanics........................- Waves........................- Electricity...........- ChemistryA Visual Representation of The Periodic Table of the ElementsTom Lehrer's "The Elements" - Animated Version
Business - EconomicsKhan Academy's Banking and Money VideosKhan Academy's Finance VideosShane Killian's Economic Basics.............- ManagementSocial Studies - HistoryIdentifying the real thing....................- LawShane Killian's Constitution Lectures....................- Politics....................- Pop Culture....................- Psychology & SociologyPsychology of BeliefMathematics - GeometryKhan Academy's Geometry VideosKhan Academy's Trigonometry Videos..................- AlgebraKhan Academy's Pre-Algebra VideosKhan Academy's Linear Algebra VideosKhan Academy's Algebra Videos..................- CalculusKhan Academy's Calculus VideosKhan Academy's Differential Equations Videos..................- StatisticsKhan Academy's Probability Videos..................- ArithmeticKhan Academy's Arithmetic VideosLanguage - Rhetoric - Debate - FallaciesNizkor's List of FallaciesWikipedia's List of FallaciesTaxonomy of logical fallaciesYourLogicalFallacyDebunking HandbookA Concise Introduction to Logic
.........................................- Examples.........................................- Inductive Vs. Deductive............................- Public Speaking (Dos and Don'ts)..............- Foreign Language (Translators)Google's Foreign Language TranslatorYahoo's Foreign Language Translator..............- GrammarNotorious Mix-Ups in Grammar..............- Dictionaries, Thesaurui, and Other Word-Storage..............- QuotesDailyAtheistQuotePositiveAtheismCreativity - Arts - Music
-bands, how-to, etc-.......................- VisualTails-155's deviantArt-deviantArt, Worth1000, etc.
.......................- LiteraryStorm by Tim Minchin
-book review sites, etc.
Ebon MusingsRichardDawkinsdotnet list of suggested reading..............- Problem Solving (how to think outside the box, etc.)CreatingMindsSkepticismShane Killian's BogosityThe James Randi Foundation YouTube PageRichard Wiseman's YouTube PagePenn and Teller's Bullshit!
Richard Wiseman's HomepageNeurological BlogSkepticalScienceC0nc0rdance's BlogProjectReasonActivismMikipedia's I Am An AtheistRichard Dawkins: An Atheist's Call to ArmsIMRational's Why Do Atheists Care About Religion?GoGreen's Why Atheists Care About YOUR Religion20/20's The Price of AtheismZakieChan's AtheistCeleb AtheistsTARGETS-CreationismTalkOrigins ArchiveNCSE's WebsiteAronRa's Foundational Falsehoods of CreationismThunderf00t's Why Do People Laugh At Creationists?,
Shane Killian's Homage Videocdk007's Evidence FOR Evolution and Against Creationismcdk007's Why Young Earth Creationists Must DENY Gravitypotholer54's From Big Bang to Us -- Made EasyDonExodus2's Transitional FossilsDonExodus2's The Way of The Master- Lies and Ignorance ExposedHow Evolution Works - Including How Abiogenesis Works
cdk007's Evolution is a Blind Watchmakercdk007's How Wrong are Young Earth CreationistsShane Killian's How Evolution is Scientific............-Conspiracy Theories9/11 Conspiracies Debunked............-Religion-Related Senseless Practices (Abstinence Only, Circumcision, etc.)Jezuzfreak777's Who Wants Atheist For Friends?(sic)
............-General IgnoranceWhat's The Harm?Fun With The AboveThe Crackpot TestHundreds and Hundreds of Proofs for GodLaws, Corollaries, and Vocabulary of Debate and MailWall of Shame at WWGHA?Philosophy- or Science-Comics and other fun stuffSci-ence - Comic
NerdyDayTrips - Locations you might want to visit
Symphonies of Science - Autotuned science-music
PHD-ComicsSaturday Morning Breakfast Cereal - Comic
XKCD - Comic
What if? - XKCDCalamitiesOfNature - Comic (No longer active)
Miscellaneous - Better Education............-Videos on YouTubeShane Killian's Why Don't We Know More? A New Year's Resolution for HumanityShareski's Education Today and TomorrowJSTD4's Pay AttentionCanadian Cancer Society - A playlist on the research on cancer
............-WebsitesKhanacademy - Mathematics
Hersperian - Free resources on health
Cochrane collaboration - A research group doing meta-analysis on health-care
AnimalDiversity - Free teaching/learning material
Learner - Free teaching/learning material
Coursera - Free University courses
List of Open-access science journals (Meaning they're free)
ScienceStore - Science explained with material (pictures are excellent)
Evoled - Teaching Evolution
Understanding Evolution - BerkleyOpen Yale Courses - Free courses at Yale University
............-ToolsUnsourced - A PlugIn to help you find out where the research for an article came from
YouTube Check-it list - WebsiteIntroducerat - Evolution - A continually updated website with videos about evolution
YouTube Check-it list - LeadersAndromedasWake - CrAP Debunked, Welcome to the Universe and
SiriusStargazingAntiCitizenXAronRa - Foundational Falsehoods of Creationism
beautyintheuniverse - Thunderf00t
cdk007C0nc0rdance and
C0nc0rdanceAnswersDonExodus2 - How Evolution Works, How Abiogenesis Works
DPRJones - Creator of the
MagicSandwichShowDPRJonesLivesdjarm67ExtantDodo - LOTS of refutations
JaguarJ0nes - How to Pwn a YEC
JRChadwickMagicSandwichShowMikeFoz - ToBeFair
MinutephysicsNational Center for Science Education (NCSE)Potholer54 - Made Easy
Potholer54debunks Creationist Crap Debunked
QualiaSoupTheraminTreesTh1sWasATriumphThunderf00t - Why Do People Laugh at Creationists?
ZOMGitsCriss............................. - OthersAKG41470Albert10110AmazingMeetingVideos - Official page for The Amazing Meeting
AnimalPlanetTV - Animal Planet's official channel
AnswersinbooksASPCA - the official video channel for The American Society for the Prevention of Cruelty to Animals
AtheistBlindChick - self proclaimed aphilatelist
AtheistExperience and
TheAtheistExperience - channels for The Atheist Experience, a local TV show in Austin, Texas
Best0fScienceBotAttack - one of the anti-censorship pages
DesertphileDiscoveryEducation - Discovery Education's official channel
DiscoveryNetworks - another Discovery channel
DMCAAbuse - another anti-censorship page
DrixDZanthEdwardCurrentEvilZoeExpelledExposedEvoBiologistFactVsReligionFFreethinkerFirstFreedomCampaign - the official page for the First Freedom Campaign
FranzDuckVideosFreeScienceLecturesfreedom0f5peechFightingAtheistGIIVideo - Creator of the website
Why Won't God Heal Amputees?GreatBigBoreGoGreen18 -
LaciGreenimrationalJamesRandiFoundation - The James Randi Foundation official channel
KeepFreeSpeechFree - My Secondary Account
klomckin - hosting many things on Bible errors
Largo64LiberalViewerMeolodysheepMickipediamorsec0de - presently hosting Here Be Dragons
NationalGeographic National Geographic's official channel
NonStampCollectorOminousVoicePatCondellPennSays - Penn Jillette's official page for his Crackel series, Penn Says
PhilhellenesPironiroquirkology - Richard Wiseman's official channel
RabidApeRationalResponseResearchChannel - The Research Channel's official...channel
SauceNMeatballsSchrodingersFinchScienceChannel - the official Science Channel...channel
ShwanerdSolRosenberg84TEDTalksDirector - official channel for TED
Teirusu155 - My primary account
TheAmazingAtheistthecarruthsTheDarwinFinchesTheGunpowderTreasonTheologikosTheoreticalBullshitTheWayOfGrowingPainsTreadTheeNotXenuTVXenuExposedYorrikeBooks/DVDs/non-websites still would go with their respective section, not art->Literary etc
"Sometimes people don't want to hear the truth because they don't want their illusions destroyed." ― Friedrich Nietzsche
"I shall achieve my objectives through the power... of Science!" --LessWrong