With the Dreamcast, since you’re going through VGA, make sure you set 480p in sampler to DTV 480p, otherwise the aspect ratio is going to be wrong.
Regarding the PS2, I believe what you’re seeing is overscan. On CRTs, those black areas are usually drawn beyond the viewable screen area; but modern flat-panel displays (LCD, [O]LED, etc.) will display the full frame. If you don’t want to see the overscan areas, you can try playing with the aspect ratio setting in the system settings menu, but I believe you’ll need to either use your TV’s zoom functionality or get a secondary scaler that can handle zooming or cropping of overscan; the OSSC was not designed for that kind of image manipulation.
For the Xbox, someone more experienced may need to chime in, but I think it could just be poor scaling on the part of your TV. Does your TV definitely recognize the signal as PAL60, or does it think it’s NTSC? Generally, I recommend using a softmod to change the video region to NTSC, so you can take advantage of 480p, 720p, and 1080i.