Here's an article that Teller, of Penn and Teller, wrote for Smithsonian Magazine about the cognitive behaviour that stage magicians exploit to fool you. There's a lot in it that's of value to referees of adventure games as well.
Chris Pound's name generators. I forget who linked to this the other day, but I found it extremely interesting. Contains a lot of roleplaying setting specific stuff, like if you need some Tsolyani gibberish.
Synergon. I've never been sure if this is a real RPG that anyone has tried to play, or if it's just an elaborate parody.
Exosolar, which is my go to map for harder types of sci-fi, and is the source that caused me to change Traveller jump distances to xe parsecs, where x is the whole number of the jump-drive rating and e is Euler's number. 1 parsec of travel won't even get you to Alpha Centauri.
Fordham University's historical sourcebooks are excellent for research. I'm only going to link to the Ancient History one here, but they have a medieval one, as well as decent coverage of a bunch of non-Western civilisations. Well worth checking out for research for historical games or for when you're creating a pastiche of historical civilisations.
Where I get all my hex paper from.
A dice probability calculator. I've been meaning to write something more extended on the subject, but I think it's tremendously important for referees to know or quickly calculate the probability of some die result or threshold so that you can set difficulties for tasks quickly and fairly. A tool like this is extremely useful if you like games with non-percentile resolution mechanics (I'm a Traveller fan, for example). This one is good because it will check thresholds for you when you click on "At Least" or "At Most".
Just a ton of useful information on various real world languages if you're looking to have your fantasy language sound different than English.
I keep on meaning to construct a whole bunch of languages for the Dawnlands, except I think it would come across as even more obsessively detailed than it is now. This is what I would use if I was to design them though.
Runequest enemy creator. I think this is compatible with MRQII, although I think it was created for MRQI.
Of all the various interesting things Isomage has on his website, the cave generator is the one I like the most. I used it to create the cave maps for Warren of the Leper Queens.
When I run a game set in medieval times, I send this website to the PCs to help them pick names.