Making crosswords

To create crosswords for guided reading, I use the site
http://www.armoredpenguin.com/crossword/.

This site provides you with lots of options for generating the crossword. The key one is to set to grey squares, as otherwise you will eat toner cartridges in printing them out.

Also, don't forget to set PDF page size to A4 from US Letter.

When you have created the puzzle, use the "Printable PDF" button to generate a final version. You will probably want to save the Answer Key as well in case there are any problems or questions.

Other resources

The Smart Crosswords site has a pretty large collection of ready-made kid friendly crosswords.
I discovered that the Teacher's Corner has a good crossword generator too. They also have some sets of pre-made clues, so you may be able to generate a crossword from those clues to save even more time.
There is another generator called Crossword Labs that has saved crosswords, with a searchable index, but unfortunately the answer keys are protected by passwords, so you can't really check the saved crosswords for quality.
There is a generator at http://tools.atozteacherstuff.com/free-printable-crossword-puzzle-maker/ but I haven't tried it out yet.
Discovery has a "criss-cross" generator that seems to generate good inter-connection but makes no attempt to fit the clues on the same page as the puzzle.
The classhelper.org.uk crossword generator appears to make good interconnects, but doesn't have a simple answer/clue loading function, and PDF generation seems to be broken.
The ABCya.com crossword generator interconnects well, and has a simple import function, but limited options for altering the puzzle.

Alternatives

readwritethink.org has a good crossword generator too at http://www.readwritethink.org/files/resources/interactives/crossword/