Virtual Library – American Indians is a list of Native American resources on the internet. The links are not particularly well organized, but they are kept relatively current.
The Alamo includes a map of Texas in 1836, biographies of the participants in the Battle of the Alamo, and photo tours of relevant locations. A nicely comprehensive website whose only weakness is a degree of hero worship (and accompanying bias).
U.S.-Mexican War includes a timeline and a discussion board, but the real meat of the site is in the “dialogues” section, where various historians provide their sometimes conflicting takes on subjects like Santa Anna, James K. Polk, manifest destiny, and the aftermath of the war.
Historynet has dozens of articles about the Old West. Since the articles come from Wild West Magazine, they are well researched by competent authors. The site also contains sections about other areas of American history, including the Civil War.