How do I check for a css value using jQuery?

Looks like it gets returned in the form rgb(x, y, z), so your code should be:

$("#tracker_table tr#master").click(function(){
  if($(this).css("background-color") == "rgb(255, 255, 255)") { 
    $(this).css("background-color", "#C2DAEF");
  }
});

Edit: That being said, I'd suggest you use classes instead of inspecting/setting css properties directly. Something like this:

$("#tracker_table tr#master").click(function(){
  if(!$(this).hasClass("selected")) { 
    $(this).addClass("selected");
  }
});

Css:

tr { background-color: #FFFFFF; }
tr.selected { background-color: #C2DAEF; }

While this may work, in effect you are storing information in the form of colors, and then retrieving and comparing this information later. Alconja suggests an approach that will work, but ultimately you may be better off working with classes, whose names can be defined by you to carry appropriate meaning. It's much friendlier and less brittle to have something like this:

$('#tracker_table tr#master').click( function(){
    if ( $(this).hasClass('something') ) {
        $(this).removeClass('something').addClass('something_else');
    }
})