Women can't be studied apart from the broader history and literature of their time, but there are a variety of online resources that have been developed specifically to illuminate medieval women's experiences, literacies, and writings. In addition to the sites linked below, you'll want to consider the resources provided for the women writers gathered on the Major Authors page as well as those on the History and Culture page (esp. the sections on "Love and Sex").
The British Library: Learning website has a section dedicated to medieval women.
McMaster University has developed a "Medieval Women" website, providing introductions to both laywomens' and nuns' lives. It is richly interactive (but somewhat older, so not all of its features still render well). The "Scriptorium" feature is particularly useful.
The British Library's "Timelines" website is an interactive flash website using treasures from the British Library's holdings to illustrate different aspects of everyday life, high culture, and political events (medieval through the present day). To focus on medieval women, after you have launched the main Timeline choose the "Everyday Life" timeline at the top of the interactive Timeline page; the site will highlight features of everyday life that may help further your understanding of medieval womens' lives (like pregnancy, literacy, and nunnery culture).
This Women Religious in the Middle Ages pathfinder from UNC-Chapel Hill is slightly out of date but still a useful starting point for researching medieval nuns and anchoresses.
Feminae is a bibliographic index (like the MLA) to books, chapters, and articles written on all aspects of medieval women and gender. Extremely useful for doing research on medieval women.
Epistolae, a collection of medieval letters (many in translation) by medieval women across Europe (c.400-1300), plus biographies and additional information about these women. Originally conceived by Joan Ferrante.
The Monastic Matrix website is a high-powered scholarly resource for studying female religious communities of all types across Europe, from c. 400-1600.