Change highlight colour in Sublime Text 3?

With the new .sublime-color-scheme format, it's a global setting key named line_highlight e.g.

{
    "name": "My colour scheme",
    "globals":
    {
        "background":     "rgb(0, 0, 0)",
        "foreground":     "#aaaaaa",
        "caret":          "red",
        "line_highlight": "#222222"
    },
}

Tony Vincent's answer is excellent, and I would also add that if changing the selection color makes the selected text difficult to read, selectionForeground is the key to change. For example:

<key>selectionForeground</key>
<string>#000000</string>

You can see which theme you are using by going to

Preferences>Colour Scheme

and see which one is ticked.

Open the theme file and find the key that says:

<key>selection</key>

Go to a site that shows hex colour codes (like this one http://html-color-codes.com/) and find the code for the colour you want. Then sub your new colour code into the line below the selection key in the theme file, replacing the old hex colour code.

Save the modified theme file and it should work straight away.

EDIT
Install PackageResourceViewer plugin using package control. Open the command palette with ⌘⇧P (for windows/linux CtrlShiftP) and type prv to get the PackageResourceViewer options. Choose Open Resource >>Theme- YourTheme >> and edit your theme file