I'd like this to become a catalog of links (to both web sites and old-fashioned tree-bit-type books) both deep and broad enough to help in the struggle for emunah. Please feel free to suggest other resources that people might find useful.
As I've mentioned a good few times through the pages of this site, Rabbi Dr. Dovid Gottlieb's online resource, Living Up to the Torah is pretty much state of the art in the evidence-for-Torah department. Can't think of anything that comes close.
If you prefer something solid you can hold in your hand rather than reading off a computer screen, they've done a rough job of converting the material into a print-on-demand book that can be purchased (at cost) here.
As much as as I might be inclined to, I just can't find any kind of fault with The Shmuz. Here you will find a community of sincere, uncynical growing bnei Torah from all walks of life led by Rabbi Shafier, a sincere, uncynical growing ben Torah (coincidence? I wonder...). You just can't help but grow with them.
And who can argue with a web site (torahanytime.com) that exists only to freely provide hundreds of thousands of hours of inspiring Torah to as many people as they possibly can? This one has "emunah" written all over it.
One way to kick-start a relationship with the Torah-world of Rabbi S.R. Hirsch is to read the work he published first. The Nineteen Letters" was written to serve as an introduction to, and overview of Hirsch's philosophy of mitzvos within the context of the historical forces that he felt made his entire life's work necessary. Rabbi Josef Elias' extensive notes to this particular edition (while arguably taking rather narrow positions on some areas of ongoing debate), is irreplacable.
If you're serious about achieving the kind of sophisticated immersion in Torah life that Hirsch's writings can inspire, there's no substitue for his larger works: The Hirsch Chumash and The Hirsch Psalms.
One more Hirsch resource: "Tzvi Tifarto - The World of Hirschian Teachings" contains surprisingly good essays by contemporary rabbonim on Hirsch's work and impact. (I had always known that the Novominsker Rebbe had been rosh yeshiva in Washington Heights for some years, but I always assumed that he was just there to give shiur. It turns out that I was - yet again - wrong: Rabbi Perlow really does understand and love Hirsch on his own terms!)
Rabbi Aharon Feldman's "The Juggler and the King" ("An exciting expansion of the Vilna Gaon's powerful ideas on the purpose of Creation, the Jewish People and its history and destiny, and the coming of Mashiach.") is the kind of book that, through its multi-level intelligence, can answer all kinds of questions by talking about entirely unrelated subjects.
For a breathtaking view of the subtly comprehensive nature of Torah, good quality time with Rabbi Tzvi Hirsch Schlaz' "Sefer Niflaos m'Toras Hashem" is good quality time well spent. You can freely download both volume one and volume two at hebrewbooks.org (my favorite website).
As I've mentioned before, I have neither the desire nor the ability to take sides in the Torah/science debate. However, that doesn't mean you can't. "The Science in Torah" by Yehudah Levi is an interesting book on the subject that touches on many of the key issues while remaining (fairly) safely under the radar.
Despite the fact that it contains a couple of scenes that are mildly inappropriate and the fact that Christian-Jewish debates are certainly not the focus of our web site, the DVD of the BBC film, "The Disputation" has a lot to recommend it. The screenplay is both smart, and loyal to the Ramban's own account of the debate. Many crucial issues of emunah are very clearly and convincingly presented. And the acting is professional (not a cringe-inducing moment in the whole thing).
What exactly is necessary to create a relationship with God through tefila? This essay examines what a direct connection should mean...and how to balance this against seemingly contradictory gemaros.
Read superficially and without proper attention to both detail and context, midrashim can sometimes seem strange - or even silly. These essaysexplore some of the rules and methodologies that can uncover the subtle beauty of midrash.