What are the differences between a cover letter and an application letter? I would like to apply for a PhD position, and I have found the following requirement in their web page:

An application letter that includes at least:


contact information of the applicant
the topics of interest in ranked order 
names and contact information of two senior academics available for reference per e-mail,
information whether the application can be used in filling other vacancies at the Department and,
from which source the applicant received the information regarding the current call.


I was thinking to put all these items in a list and fill them like some type of survey, but I am dubious if I should do that. I mean I have found templates for cover letters, but not for application letters. Is there any format for this?
Good question, and has been something that I have been thinking about also.

Digging around, I found a few articles that may be of assistance, This eHow article (Even though it is more trained towards work, rather than academia), and thi about.com article.  

Both links state that there are subtle differences - specifically, an application latter explains what qualifies you for the position/study, and the cover letter goes into more detail as to what qualifies you and explains your interests in the position/study.

I hope this helps (and best wishes with your application and studies!)