Large archives

The number of alchemy texts already online is scarcely believable, since the entire body of work as literature has been largely forgotten, nevermind the comsological/philosophical aspects. Still, according to Adam McLean, only 1% of extant texts are online.

Take some time to browse around these sites:

Adam McLean's Alchemy Site
The primary online source, massive and well-categorized.

Rex Research Alchemy pages
There is a lot of overlap here with Adam McLean's site, but Robert Nelson has several texts not found elsewhere, including Mary Anne Atwood's Hermetic Philosophy & Alchemy and the influential Ordinall of Alchimy by Thomas Norton.

The AZOGUE journal maintains a large archive.

Alan Pritchard maintains an extensive biliography, including a section for online texts.

Relevant texts can also be found at the Internet Sacred Text Archive in the alchemy, freemasonry, Rosicrucian, and sub rosa sections.

European Cultural Heritage Online, many interesting source text scans.

The Twilit Grotto, etexts of many of the most important Renaissance thinkers, John Dee, Agrippa, Johannes Trithemius, Giordano Bruno, etc.

Lullian Arts has hypertexts and applications relating to Raymond Lull's mnemonic techniques.

The Newton Project is digitizing some of Newton's more speculative and theological writings that have seldom been seen before. Also Robert Boyle's work diaries are online.

Theatrum Chemicum Electronicum (1st ed. 1602), an electronic reproduction of Lazarus Zetzner's 6-volume >5000pp compendium, mostly in Latin. Electronic edition by Rafal Prinke. Not to be confused with Elias Ashmole's Theatricum Chemicum Brittanicum (1652). The UPenn images of Ashmole's collection have been collected into a pdf.

The Complutense University of Madrid has around 120 manuscripts (mostly latin) online, including Bibliotheca Chemica Curiosa, compiled by Jean-Jacques Manget.

The Manly P. Hall manuscript collection is now online at archive.org

Berthelot's Collection des anciens alchimistes grecs:
Vol. 1
Vols. 2-3
Vols. 3-4

C.G. Jung's alchemical collection is also currently being digitized.

The Swiss site e-rara has the Alchemy, Magic and Kabbalah (Foundation of the Works of C.G.Jung) and Historical scientific literature (ETH-Bibliothek)

I would also like to point out Mike Dickman's original translations and the R.A.M.S. collection, which is not online, but can be ordered on CD-ROM.