Personally I always felt that after Stanford and Jessica, and the deaths of his father and then brother, Sam just... slowly began to stop caring about his appearance beyond the basics. If this is what your life is going to be, why bother? In the later seasons, it's almost like he increasingly didn't want folks to look at him too closely - or to look at him and dismiss him. Most of his wardrobe indeed screams "remaindered at Walmart" or "only $2 at Goodwill". The fact that some looks good seems pure random chance.
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Personally I always felt that after Stanford and Jessica, and the deaths of his father and then brother, Sam just... slowly began to stop caring about his appearance beyond the basics. If this is what your life is going to be, why bother? In the later seasons, it's almost like he increasingly didn't want folks to look at him too closely - or to look at him and dismiss him. Most of his wardrobe indeed screams "remaindered at Walmart" or "only $2 at Goodwill". The fact that some looks good seems pure random chance.