If you ever stumble upon the missing 'Upload' button in the File Manager the first thing you should check is your 'Allowed File Types'. More often than not, the issue stems from the fact your installation no longer accept any file types to be uploaded (the setting has been wiped).
(Editor's note: This issue was caused by faulty code released in the HTML5 Music and HTML5 Video add-ons. The installer code for these add-ons attempted to add new file extensions, but accidentally removed everything from the list instead. The developer has addressed the issue in a later release. This problem is not caused by upgrading the concrete5 core. Check out this thread for more info.)
In earlier versions of concrete5 you had to define your allowed file types in your 'config/site.php' file, but that is no longer needed. Nowadays all you have to do is open up your dashboard and go to 'System and Settings'. In the 'Permissions and Access' section click on the link 'Allowed File Types'.
After you click that link you can add all the file types you want your file manager to accept.
The file extensions you see in the image above are the basic ones which should come with your concrete5 installation by default. If they are lacking in your setup you can copy them from here and paste into your system:
flv, jpg, gif, jpeg, ico, docx, xla, png, psd, swf, doc, txt, xls, xlsx, csv, pdf, tiff, rtf, m4a, mov, wmv, mpeg, mpg, wav, 3gp, avi, m4v, mp4, mp3, qt, ppt, pptx, kml, xml
As you might have guessed, you can also add other file types you might need if they are not listed above.
Once you hit 'Save' the 'Upload' is accessible and you can start uploading your files.