My web app is using a large icon set with jquery-ui and jqgrid.
In order to easily maintain the changes to the CSS to accommodate the larger icons when upgrading jquery-
If you include each file individually, the bundle will respect your order...
var bundle = new Bundle("~/Content/dark-hive/allstyles", new StyleBundle());
bundle.Include("~/Content/dark-hive/jquery-ui-1.8.23.custom.css");
bundle.Include("~/Content/ui.jqgrid.css");
bundle.Include("~/Content/jquery-ui-fixes.css");
bundle.Include("~/Content/icons.css");
bundle.Include("~/Content/site.css");
bundles.Add(bundle);
UPDATE
Even using explicit order, you'll find that there is a rather handy built-in ordering system that orders specifically named files first over all others. To completely clear this out, you can use:
bundles.FileSetOrderList.Clear();
And you can add your own custom ordering using:
BundleFileSetOrdering ordering = new BundleFileSetOrdering("My Order");
ordering.Files.Add("jquery.js");
bundles.FileSetOrderList.Clear();
bundles.FileSetOrderList.Add(ordering);
Essentially, there is a massive built-in list of files that will get put in a certain order before any file that isn't in the list - but these options let you take control.