I agree with most of what has been already advised. Pull your roommate aside (if you can get some private time when his gf isn't there, that is). Keep your personal feeling about his girlfriend to yourself and just say that you've noticed that she's there...A LOT. Tell him that you feel uncomfortable having her there when he isn't, especially when you've had a long day and just want some quiet time.
Also, perhaps in your quest to be nice to her for your roommate's sake, she got the impression that you two are friends and that she is welcome there at all times.
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AGD
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