Only a few changes at the GUI are required every thing else can be done by a local batch file (i can provide a batch for that).

Just add the "Remote Shell" option to the "Run as" dropdown. 
Copy all fields from "Remote Web Site" to this new run as option.
Replace "Project URL", "Index File" and "Arguments" by the following fields of the "Script (run in command line)" run as configuration:
- "PHP Interpreter" (rename it to "Remote Execution Proxy"
- Arguments

On "run" pass "Arguments", "Server Path"*, "Project Path"*, "Host name"**, "User name"**, "Password"**, " and file to run as parameters to the "Remote Execution Proxy".

* = from Path Mapping in Advanced Web Configuration Dialog
** = from the selected "Remote Connection"

Output of the "Remote Execution Proxy" should be forwarded to the "Output Window" as normal.

Everything else can be done by a local batch file using putty plink and putty pscp (putty is availabel for unix (mac) and windows).

Optional: the following fields would be nice to have:
- PHP Interpreter Path (local) with browse button
- PHP Interpreter Path (remote)
- SSH Client Path (local) with browse button
- SSH Client Arguments
- SCP/FTP/SFTP Client Path (local) with browse button
- SCP/FTP/SFTP Client Arguments 
All of these should be passed to the Remote Execution Proxy, too.

This feature would be nice for all developer working running netbeans on a windows system while want to test the php scripts on a (remote) unix system, too (on development). May be there are Mac/Unix users that want to test their scripts on a windows server, too. 

I am willing to provide a working batch that i use at the moment by using the run as script configuration, but "upload to remote on save" is missing and aviod me from beeing productive (i don´t want to swich the run as configuration on and on).

My batch can be extended to be able to start and stop "debug sessions" as well.

If your roadmap does not allow to add it into the 7.0beta3 it would be nice to see it as an extension (nightly build).

At a later step (if you want to spend more time on it) you can add a tighter integration with the internal scp / ssh clients or by adding putty to the bundle.