"Avigation" is aerial navigation; the word was coined from a combination of the stem "avi-" (for "bird") and "navigation." As a user of AWADTalk, A.Word.A.Day's discussion forums, put it:
Finding a distant destination used to be an extremely challenging task. In WWII, a huge flight of Air Force bombers set out to destroy oil refinery at Ploesti, Roumania. There was cloud cover almost all the way. They missed the target by hundreds of miles...The cause was not discovered until long after the war - the now well known jetstream. Now GPS makes knowledge of position of aircraft constantly available with fantastic accuracy. And detours around bad weather zones can be made with important savings in time and money, using information from electronic communications. That's avigation.
Among non-pilots, the word seems to be most commonly used in the phrase "avigation easements," which are agreements granting airplanes the right to fly over a piece of land. These are usually only an issue for property near airports. An airport might need to obtain an avigation easement "when its operations interfere with a neighboring property owner’s right to full enjoyment of his or her land" (such as excessive noise). However, after it's put into place, an easement allows any flights that follow the rules set out in the easement, even if they cause damage, inconvenience, or loss of property value. These easements also generally restrict the property owner from building or growing anything over a specified height.
Avigation.net is the future URL for the World Aeronautical Database, an online resource that gives information to help in reaching airports and navaids worldwide. "Avigation" is also the name of a line of watches by Longines.
Sources:
http://wordsmith.org/awad/archives/0803
http://www.tiscali.co.uk/reference/dictionaries/difficultwords/data/d0001860.html
http://www.foreclosuresmass.com/help/view/glossary/termid/79
http://www.eltoroairport.org/issues/aveasement.html
http://www.eltoroairport.org/issues/aveasement2.html
http://www.bankrate.com/brm/definitions.asp?Page=2&channelId=27&slid=1&termUid=2354
http://worldaerodata.com/
http://www.bc.edu/schools/law/lawreviews/meta-elements/journals/bcealr/28_2-3/04_TXT.htm
http://www.wordsmith.org/board/showflat.pl?Cat=&Board=weeklythemes&Number=111509&page=18&view=collapsed&sb=5