The easiest way to get a report of all checked out files is by using powershell script as described in the blog
http://www.sharepointdiary.com/2013/02/find-all-checked-out-files-and-check-in.html
Another option is to use web services see below blog for reference
http://sqlblogcasts.com/blogs/drjohn/archive/2007/11/02/Getting-a-list-of-files-from-a-moss-document-library-using-a-SharePoint-web-service.aspx
Also This blog mentions a very easy way to create a report of all documents which are currently checked out in a site it is listed again here
http://www.sharepointdiary.com/2013/02/find-all-checked-out-files-and-check-in.html
Another option is to use web services see below blog for reference
http://sqlblogcasts.com/blogs/drjohn/archive/2007/11/02/Getting-a-list-of-files-from-a-moss-document-library-using-a-SharePoint-web-service.aspx
Also This blog mentions a very easy way to create a report of all documents which are currently checked out in a site it is listed again here
1) Go to (out of the box) List 'Content and Structure Reports' and add a New Item.
2) Fill the following values:
Report Title : CheckedOutFiles
Resource Id : SmtCheckOutUser
Resource Id : SmtCheckedOutReportDescription
CAML List Type : <Lists ServerTemplate="101"/>
CAML Query : <Where><Geq><FieldRef Name='CheckoutUser' LookupId='TRUE'/><Value Type='int'>0</Value></Geq></Where>
Report Description : All documents and pages checked out in this site and subsites
Resource Id : SmtCheckOutUser
Resource Id : SmtCheckedOutReportDescription
CAML List Type : <Lists ServerTemplate="101"/>
CAML Query : <Where><Geq><FieldRef Name='CheckoutUser' LookupId='TRUE'/><Value Type='int'>0</Value></Geq></Where>
Report Description : All documents and pages checked out in this site and subsites
3) Navigate to Site Settings -> Site Administration -> Content and structure
4) This gives context to the right-hand window where you can look at views and manipulate content in certain ways.
5) If you click on view: and choose the latest added 'Content and structure' item you can view all the documents checked out in all the document library in the site and its subsite