Use WhizFolder Organizer for your text notes. Fully functional evaluation versions are available for download. Many of the texts are onsite here and unique in the web. Also includes German, English, and Greek literature. Bibliotheca Latina - From the University of Wisconsin.
Page is entirely in Latin.
Unfortunately, all but Boethius' Consolatio Philosophiae are restricted to use by students at the University of Virginia. Labyrinth Latin Library - A collection of ancient and medieval Latin texts, but some gopher links are outdated. Pliny's Natural History, Frontinus, Vitruvius, Ptolemy's Geography. Layout is a bit daunting, but there's a LOT of texts here. Lupa - Helps for searching for classical texts.