- An amazing book called _[Seder Hakorot BaTana"ch][1]_ written by Eliezer Shulman, a _Tana"ch_ scholar of the 20th c. has maps, charts, timelines, and genealogies with extensive and careful explanations, including multiple opinions or versions where necessary, all informed by the words of _chaza"l_ as well as the modern (Bar-Ilan-type) lay scholars. It is a large format book and the text is penned in the author's own incredibly consistent handwriting. It bears *haskamos* from 3 chief rabbis as well as noted Biblical scholar Chaim Gevaryahu. It has been translated into English as well, with minor formatting editions to the text, under the title *[The Sequence of Events in the Old Testament][2]*.
 - A fun "book" I believe is called Midor L'dor that is actually a (40ft.) foldout timeline of _Tana"ch_ with some colorful illustrations. It may seem juvenile but it serves as a great visual counterpart to the conceptions of timespans found in the Torah.
 - _[Atlas Da'as Mikra][3]_ (mentioned above by @msh210) is a good atlas for reference. It may not have all the detail you are looking for when it comes to the ins and outs of _kibush ha'aretz_ but it has clear maps for every occasion. (I find it a little frustrating that it gives the impression of being "missing" a lot because they don't print anything they are not really confident in the veracity of.)


  [1]: http://www.booksefer.co.il/index.php?dir=site&page=catalog&op=item&cs=14395
  [2]: http://www.amazon.com/Sequence-Events-Old-Testament/dp/9650502688/ref=sr_1_1?ie=UTF8&qid=1308258800&sr=8-1
  [3]: http://www.mosadharavkook.com/store/item2.php?id=50