GetHT downloads PDF files from Hinduism Today, an "award winning, Macintosh-generated, full color quarterly news magazine articulating Indian spirituality for 135,000 readers around the world." It is the only native GNU/Linux client available, has good proxy support, and allows you to only download the parts of the magazine that interest you.
Qirat Quran Reciter allows the user to read, search, and listen to the Quran (a.k.a. Koran or Coran). Many translations are available (including English, French, Spanish, Turkish, and Indonesian) and no audio plugin is required. It includes many features and an easy-to-use interface.
Torah Tools is a collection of utilities designed to assist Torah learning. Currently, Torah Tools consists of two programs: Daf test and Gemarah charts. Daf test helps you memorize on what page each Gemarah is to be found. It gives you a test to take after you learn a Perek or Masechta that requires you to choose the correct location for a displayed Amud of Gemarah. Gemarah charts helps you keep track of how many times you've Chazered over material by providing a chart with a list of all of the Perakim in the Mesechta, a list of the Dafim in each Perek, and just enough room in each box to mark off your Chazaros.
Salvation Focus is an application that encourages a group of people to pray for others they know who do not know Jesus Christ as Lord and Saviour. Salvation Focus is a small Flash application that can be included on pretty much any Web site. There is also an administrative interface for adding people to pray for, the people that asked for prayer, and some contact info.