Go to site actions -> Manage content and structure. At the first page there is a list of the files with a "view" in the toolbar on the right section. Drop this down and choose "Checked out to me".

This will list all the files, you can then check the checkbox to select all items and in the actions drop down choose check in.

Go to Site Settings -> under Site Administration, select "Content and Structure". At the first page there is a list of the files with a "view" in the toolbar on the right section. Drop this down and choose "Checked out to me". Navigate to the folder where the files you wish to check in are located.

This will list all of the files checked out to you in the given directory you are in, and then you can check the checkboxes to select your items and in the actions drop down choose check in. You'll be prompted one time for the comment to check the file in with, so be sure you want to replicate that comment across all selected items for the Version History.