Here are links to a comprehensive collection of Jewish E-books. There are ample resources for ספרים online yet there existence is almost a secret. Just like your house should be filled with ספרים your computer should be filled with ספרים. Besides, it's free.
Two years ago I decided to get an E-reader and fill it with ספרים because I assumed it would be cheaper than physical books and I could take all my ספרים back and forth from ישיבה with ease. To my dismay I was unable to find anything. It seemed nobody learned with E-readers. I decided I would change that. I tried to get Amazon to develop such a product. They completely ignored me (damn you amazon!) but the project wasn't a complete loss. As I tried to get people involved in the project, the discussion would inevitably lead to URLs with ספרים, if not for E-readers for computers. Some of the sites had links and links begot more links until I didn't even have the time to follow them all. Even though I don't have digital ספרים on an E-reader, I have the next best, ספרים on my computer. Here are the links which I have followed so far. I would like to thank the many contributers (you know who you are) and request that if you know of a site not on this list please leave a link in the comments.
Huge library of ספרים for viewing and for download. Plus they have a beautiful HTML ש''ס with רש''י and תוספות (not for download). It also has good search options.
Over half of משניות with translation and ברטנורא commentary (not translated). They are working on the rest.
Prayer books of many נוסחות including נוסח אר''י. Read the instructions on how to use text versions if you don't want pdf.
Chabadniks can download their weekly דבר מלכות in pdf.
The Lubavitcher Rebbe's חסידות and responsa. Insert the entire provided URL unless you both use IE and are interested in browsing by topics selected by משיחיסטים.
Machon Mamre has some important ספרים for viewing online and a ספרים application for viewing off-line. They also have an encyclopedia of Torah basics. They copyright their work and specifically request on the home page not to make a bot and download their whole site.
Older ספרים which are no longer under copyright. If the search doesn't work properly try the unsorted list. (some affiliation with hebrewbooks.org)
Works of the sages of Ashkenaz. It looks like a work in process.
Looks to me to be mussur and philosophy. The main site has a lot of interesting non-book resources.
Many Yiddish books. The site is in German but there is some helpful English in the lower left corner.
Oryta, a book program for computers, tablets and smartphones. It comes with a decent library which takes up a modest amount of megabytes. It is in beta so it can slow and buggy. The UI is in English and is well designed.
תורת אמת A book program for computers, tablets and smartphones. It comes with a decent library. The download is ~76MB. Before installing the locale must be set to Hebrew because it is a non-Unicode Hebrew program. Setting the local to Hebrew doesn't make your display language Hebrew. It only makes the default for non-Unicode text Hebrew. The UI is in Hebrew and I find it annoying and difficult to use.
This includes the Jastrow dictionary and Wilson's Englishmans Hebrew Dictionary. The pages are linked up for very quick indexing and referencing.
In the unlikely event that you do not know what this is, prepare for something awsome.
Excellent system of indexing. Uses both internal and external sites (hebrewbooks.org) to provide a useful system of locating and downloading the book you need in the best format available.
Large selection of rare manuscripts for download.
Huge selection of both secular and religious ספרים. Browsing by topic is well configured.
These two sites are strangely interconnected. They have got some interesting works ranging from recent religious texts to old nonreligious Hebrew historical documents. Parts of the sites are in English and Parts are in Hebrew. Similarly, some of the works have English and some don't. Not downloadable content.
This is a search engine which basically uses special google searches. Topics which can be searched are: Audio Shiurim, Books, Classic Texts, Kashrus, Q and A, Research, Video.
A catalog of all chabad ספרים. As far as I can tell this site doesn't give any access to the actual texts.
This is Torat Emet's list of links to Judaism related resources, including books, audio, and video.
Even more great content.
And even more content.