As iXue as pointed out, if using iBooks, you can drag and drop them to the Books entry in iTunes.
If using another ebook reader, the reader may support iTunes transfer via iTunes -> Apps -> File Sharing. If your ebook reader support iTunes file transfer, it will have an entry under File Sharing. You can then drag and drop ebooks here.
Most 3rd party ebook readers support network ebook downloads.
Some ebook readers work with Calibre for transferring ebooks between your computer and your iPod Touch
Calibre (ebook management/conversion utility)
ebook reader Apps: Apple's iBooks, Amazon's Kindle, Barnes & Noble Nook, eReader, Stanza, OverDrive (used by public Libraries), GoodReader (great for PDFs), Borders ebook reader, BookShelfLT
The following support iTunes App File Sharing transfers: BookShelfLT, Borders, GoodReader, Kindle, Stanza.
NOTE: Stanza is my preferred ebook app.