This is probably the least fun part of my job as a designer working with clients.
Right now I use a MS Word document template, fill in the details, and then upload to EchoSign (https://www.echosign.adobe.com/) for the client to electronically sign and then for me to electronically sign. Once we both sign, we both get emailed PDFs. It's better than faxing, but not super awesome.
What do you guys use? I have yet to try out Shake (https://itunes.apple.com/us/app/shake-app/id601561998) but I kind of like keeping my computer for work and my iPhone/iPad for fun.