Many formats are available to choose from. First determine your needs and then select a format.
Have you ever copied a document from a Mac to a PC and had Greek come up? Adobe created the Portable Document Format so people can move documents from computer to computer and the images and fonts would remain intact. As it turns out, this format is very nice for passing documents around on the web. Adobe's program to generate this is called Acrobat. Adobe's website currently sports four different versions of Acrobat, with the cheapest non-upgrade version costing $500. (The educational version is $118.) Adobe created the format and the first pdf generator, but you can create pdfs with other software.
Pdfs can be formatted the page to print beautifully standard sized papers so people can use trees. You can hit a flag in the pdf so people cannot print the document. It's easy to read these pdfs online when you're sitting at a desktop with a big monitor. Additionally, pdf has been around long enough that most people actually know how to use the documents. There are some negatives to the pdf format, however. Have you ever tried to read a full-size pdf document on a smart phone? Let's just say you need to be tenacious to do this.
epub is an open standard for ebooks, and it is designed specifically for phones and electronic readers. The software that reads the epub format allows the reader to change the font size, change justification, change colors, and change fonts. The format allows the software to resize the document for whatever device the person is using. This format is excellent for text books. This format is not-so-great for documents that have a lot of images in them.
The format is created from xml, so if you're willing to learn, you can make these without a lot of special software. However, there's plenty of software to create epub files, including Calibre, Adobe InDesign, QuarkXPress, and lulu.
The mobi format can be read on many devices, and libraries like to use this format. Mobi has methods for checkout durations that libraries need. Mobi is also cool because readers can add blank pages in their book and scribble notes. The Mobipocket Creator (home and publisher edition) is free.
Amazon's kindle is a device for reading their ebooks. Kindle emulation software is available for many smartphones and your desktop, so the Kindle format is portable. Additionally, these books can be sold in the Amazon store. The format is based on mobi, so it has a lot of mobi's features. You can create a kindle book with a free command line tool if you know a little xml. Your other option is to download a free plugin for Adobe's not-so-free InDesign. Printing from a kindle is a tad difficult, but you can always photocopy the page from the kindle.
The pdb format was created by Palm Digital Medica and is used on many smart phones. The files can be generated with eBook Studio and Dropbook. Many software programs understand the pdb format, so you can read these files on just about any type of smart phone.
Which format is best?
The format you select depends on your needs. If you're making a book of worksheets for people, make a pdf. If you're book is mostly text, make your ebook a pdb, mobi, or epub. If you want to sell the book, render your book into the kindle format or epub on lulu.