The Queued structures show up in the queue as small circular icons, to the upper right of them is a faint X.

Click the X to remove them from teh Queue.  Without a manual it is frustrating and there is a learning curve... Wait until you progress the equipment tree until your next weapons cost less and do less damage... Say What ?! yup you'll put points into research to research a worse weapon.... Intelligent  isn't it?

Yes while this was pretty obvious to many of us I suspect it's because we use many PC applications in addition to games, and it's kind of obvious and a common symbol to someone who does. But of course someone who only games on their PC and isn't to familar with desktop applications might not see it the same way.

Stardock make a lot of desktop stuff so this would have seemed natural to them.

I wouldn't be too hard on yourself, if the manual actually explained the contents of the game like it should many people wouldn't be having as many problems as they are. I'm still finding out basic things on a daily basis about this game because the manual failed to inform it's consumers properly. In fact, I'd go so far as to say that 90% of the information needed to understand this game is not provided for in the manual. They shouldn't even have wasted paper on the manual, it's that useless.

For what it is worth I'm working on a guide: http://www.gamefaqs.com/pc/954860-elemental-war-of-magic/faqs/61009

And I'll make sure my next update includes how to remove items from the build queue I also have the information from the Hiergamenon on this website (which is just the tech tree) as an ASCII chart that you should be able to copy/paste and print pretty easy. Isn't pretty but it works.

It may also be worth mentioning that you can raze individual buildings from the build queue. I've taken over enemy towns and found markets and Empire equivalents in towns without any gold production. That costs you a food for zero extra gold so I just raze them. Note that if you hover over the town you can see it's total production while selecting it or reading the summary only shows it's net production. They might use all or most of the gold or food that they produce so looking at the town summary can be misleading.

That's how I accumulated most of my knowledge of the game.  I played a lot and clicked on stuff.  Some of it was intuitive to me, some was 'strange' but I figured it out, and some was "what does this do?  Oh... good to know."  I actually found the cancel build order looking for a 'hurry production' type function (still sad there isn't one).