There is a wealth of Torah websites available for lesson preparation and presentation. These are great to share with students when giving special projects both because it will help them in their research and because it will assist them later in life when they are away in university and might not have ready access to Jewish books but will almost always have easy access to Jewish resources over the web. Below is a partial list of some of the best websites with an emphasis on Tanach.
Project Genesis D'vray Torah on the Parshat Hashavuah, and Torah lessons in Jewish Law, ethics and much more.
Shema Yisrael Torah of all types and Jewish Bulletin Boards.
The Orthodox Union You can get D'vray Torah on Parshat Hashavuah by clicking here: http://www.ou.org/torah/index, shiurim on Nach here: http://www.ouradio.org/nach, links to many great Torah sites, and Kashrut information.
Judaic Seminar Excellent Pshat based shiurim on the Humash by the Sephardic Institute in Brooklyn.
http://www.shamash.org/tanach/dvar.shtml Comprehensive list of Torah on the web.
www.tanach.org Rabbi Leibtag's site with shiurim on much of Tanach as well as Virtual Classrooms that offer multi-media features.
www.vbm-torah.org Gush Virtual Beis Medrash.
www.yutorah.org Yeshiva University's center of shiurim is mostly focused on Gemara but also has many shiurim on Parsha as well.
MJ- RavTorah List Searchable archives of weekly D'var Torah based on Rav Soloveitchik.
613.org Great audio shiurim (lectures) on many Torah topics delivered over the web as well as notes from Rabbi Soloveitchik on Parshat Hashavuah and lesson plans from Shira Smiles on Melachim Bet, Yermiyahu, and Trei Asar.
Haftorahman Background and overviews to all of the weekly Haftorahs together with lots of beautiful art, fascinating archeology, and useful timelines.
Jewish Law Articles on different topics in Jewish law.
Mechon Mamre The entire Tanach (Bible) online in Hebrew and English.
Navigating the Bible II The whole Torah in Hebrew with Rabbi Aryeh Kaplan's excellent translation and footnotes. Also includes a Tikun and an audio reading of the Parsha with Taamim as well as many other useful tools.
Page of Mikra'ot Gedolot (Torah with Commentaries) Explained A great way to learn how to navigate a page of Torah with commentaries using hypertext.