Good idea Xasthur. So here's some tips regarding panel lines. Converting these screenshots to jpeg has screwed the quality up a bit, but you can still get the general idea.
The first screenshot shows the basic panel line layers in false colours for clarity and also a light direction test layer. On the light direction layer the red arrows all line up the same way when the skin is viewed in the skin viewer. On my skins the arrows point down and to the rear on vertical surfaces and to the right and rear on horizontal surfaces. The main thing though is to make sure the direction is consistent on all surfaces.
The panel lines themselves are created in five layers, panel lines vertical, panel lines horizontal, small hatches, raised panel highlight lines and raised panel shadow lines. Splitting the main panel line layers into horizontal and vertical makes them easier to edit. So a vertical line can be moved 3 pixels to the right without disturbing any of the horizontal lines it crosses.
The raised lines are created using the light direction layer as a reference. The white lines face the light etc. Raised panels are usually things like the fairings between the wings and fuselage or in this case the bolted on armour plates on the fuselage.
Once happy with the position of all the lines its time to move onto the 3D effects. Make duplicates of the small hatches, vertical and horizontal panel line layers (not the raised panel lines) and merge these three copies into one. Switch off the original three layers as you won't be needing them except as a backup. Turn the newly merged panel line layer's lines black.
Make a duplicate of the merged lines layer and turn its lines white. This will be the panel line highlights layer. Looking at the screenshot below you can see I've carefully selected the highlight lines on each panel and moved them one pixel diagonally in the direction of that panel's arrow.
Once I've finished positioning the white highlight lines I like to delete them where they cross the black lines. To do this I move to the merged panel line layer and select all the black lines. Then I move back to the highlight layer and sweep across the whole skin with an eraser tool. This removes any part of a white line that crosses a black one.
Make another copy of the merged panel line layer, this will be the heavy panel lines. Heavy panel lines are things like landing gear doors, engine and gun hatches and control surface lines. Change the colour of the heavy layer's lines to some bright colour, I've used red on the shot below. Now simply erase all the lines you don't want to be heavy, until you are just left with the ones you want. Now change them back to black.
With the layers reduced in opacity the heavy lines are doubled up and will stand out as shown in the finished skin shot below.