For example, in a PHP file, there can be JavaScript, CSS, and HTML, so it would be really great if different parts of a file could be set as a different language for syntax highlighting and for other features.

I know that in for example Monokai color scheme there is: activeGuide key, but setting a new inactiveGuide does nothing.

The window state should be remembered between sessions. 

With my work, I always have various files open for referencing (I use 2 column view mode so I keep these files on the left, with what I'm working on on the right).  Sometimes I accidentally type something into a reference file (because I didn't realize the cursor was in there), then press control-z to undo it.  The problem is now the reference file is marked as dirty.  Since these reference files are not checked out of P4, now every time I do a "save all" I always get a dialog telling me the file is not writable.  The only fix is to close the reference file tab and then re-open it.

Hence it would be swell if when you undo changes in the file up to the last save point, it would clear the is-dirty flag :)

I feel that one should be able to give input into the build log so that build systems that offer running code aren't fed null inputs and therefore code that needs input will actually work,

{
   "shell":true,
   "cmd": ["cd $project_path && c:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319\\MSBuild.exe && $project_path\\debug\\vctest.exe"]
}

The filename, directory name, or volume label syntax is incorrect.
[Finished in 0.1s with exit code 1]
[cmd: ['cd D:\\TFS\\Scrum\\iWhiz\\Dev2.3 && c:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319\\MSBuild.exe && D:\\TFS\\Scrum\\iWhiz\\Dev2.3\\debug\\vctest.exe']]
[dir: D:\TFS\Scrum\iWhiz\Dev2.3]
[path: C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;c:\Program Files\Intel\DMIX;C:\Program Files\NTRU Cryptosystems\NTRU TCG Software Stack\bin\;C:\Program Files\Intel\Services\IPT\;C:\Program Files\Dell\Dell Data Protection\Access\Advanced\Wave\Gemalto\Access Client\v5\;C:\Program Files\Windows Live\Shared;C:\Program Files\Common Files\Acronis\SnapAPI\;C:\Program Files\CMake 2.8\bin;C:\Program Files\Microsoft SQL Server\100\Tools\Binn\;C:\Program Files\Microsoft SQL Server\100\DTS\Binn\;%TFSPowerToolDir%;%BPADir%;C:\Program Files\Prio;C:\program files\microsoft visual studio 10.0\Team tools\performance tools;C:\Program Files\Common Files\Autodesk Shared\;C:\Windows\Microsoft.NET\Framework\v4.0.30319;]

Probably already suggested, but how about allowing font size to be change by pinching on trackpad?

function a() {

} function b() {

}

The header of the function [b] won't get highlighted right though this is valid syntax.