Although I personally work with Sibelius, if you are looking for a program, you can try Finale. Both Finale and Sibelius are considered leaders in the industry today. They constantly upgrade their software and you could be sure you will get a newest version. A great thing about most music notation programs is that you can save the files in MIDI or MusicXML formats which lets you transfer them to any other notation program that you want.
Besides Sibelius or Finale, other programs available are MagicScore Maestro, Forte Home, QuickScore, QuickScore Elite, Notation Composer, NoteWorthy Composer, Music MasterWorks, and Play Music. There are some free programs, too - MuseScore, Lylipond, Finale Notepad, and Musink.
While you have to install one of these programs on your computer, wouldn't it be great, if you could do the same things these programs do but only online without the need of installation of software which can be expensive at times? Well, there are a number of online music notation services. The one that I'm happiest with is Noteflight. It's pretty new and the service is quite basic but they will certainly improve in the future.
Armed with an online or offline music notation program, a church organist can be quite productive in his music output and these technologies are without a doubt a must for anyone who wants to be successful today.