There are several editions of the complete works of JS Bach online. They are, however, bandwidth intensive to host, and sometimes disappear for a while. Here are some I know about:
The Bach Gesellschaft edition, originally published by Breitkopf & Härtel in Germany, contains almost all of Bach’s works in full score. It was published in 46 volumes between 1851 and 1900, and is public domain in the US. Multiple sites offer this for download in various formats.
- Einam.com has the complete BG in DJVU format
- The International Music Score Library Project
had the BG edition scanned and organized when they shut their doors in response to legal threats. One hopes they will have successfully resolved their issues soon.has this available, and mirrors the bh2000 collection mentioned below.
Some works are also available in vocal scores. In particular, most of Bach’s cantatas are online in this form. However, at the moment I can only identify one free source:
- bh2000 has Bach’s sacred cantatas (1-199) online in PDF format
Bach-Cantatas.com has an index of online sources for Bach’s works. Though there are some pieces for which they have no source, there are others for which they note multiple versions, including transcriptions.
A few select scores are available at the CCARH. In particular, they have Cantatas 11, 43, 48, and 213, as well as the B Minor Mass, all transcribed.
The Choral Public Domain Library has transcriptions of a number of cantatas and other vocal works.