The Medieval Sourcebook contains links to many medieval texts, theological, spiritual, literary and historical.
Early Latin Writers
Boethius’s Consolation of Philosophy is available in a very nice Latin edition. An English translation of the Consolation and several theological treatises on the Trinity in Latin and English from Project Gutenburg.
Isidore of Seville
Wikisource has De Rerum Natura.
John Scottus Eriugena
Wikisource has a few links including one to book 5 of the Periphyseon.
High Middle Ages
Wikisource has tons of Abelard texts in Latin.
Albert the Great
Grosseteste’s works are available online at http://www.grosseteste.com/
From Pasnau’s homepage there is this link to Thomas Aquinas Latin texts, but Pasnau warns that these are apparently based on old editions.
Bonaventure’s Sentences commentary is available in Latin and English through the Franciscan Archive.
Henry of Ghent
John Duns Scotus
The Fransiscan Archive maintains a fantastic site on Scotus, replete with articles and Latin texts and translations into various languages.
14th Century and Later
Peter Aureol’s Sentences Commentary
William of Ockham
Wikisource has the Summa Logicae