The text of The Faerie Queene, Book 1, was taken from Wauchope's edition, originally published in 1903. This text was chosen primarily because it was in the public domain. It was also available in an HTML format that made creating an early version of this site much easier. You can download a copy of the edition from many places around the internet.
Wauchope's edition is lacking in several respects. For one, he censored several stanzas that, apparently, he felt were a little too risqué (several lines from I.vi.22-23, I.vii.9; all of stanzas I.viii.47-48). I've supplied the missing lines with ones from the 1596 edition. Wauchope has also unnecessarily modernized some spellings.
Anyone who would like a version of the entire Faerie Queene can find it hosted at Luminarium, prepared by Risa S. Bear of the University of Oregon. The text used for this edition was The Complete Works in Verse and Prose of Edmund Spenser (London: Grosart, 1882).
If anyone is looking for a good critical edition of the text, I would highly recommend the second revised edition of The Faerie Queene, edited by A.C. Hamilton for the Longman Annotated English Poets series. In 2006, Hackett published The Faerie Queene in five volumes, allowing for easier portability.