Yes, on-camera flash in particular usually isn't the most flattering lighting. It can really take the depth out of your features and make you look flat. If you must use it, try using a setting like "night portrait" that will utilize a longer shutter speed so you can take advantage of the most ambient light possible and not rely entirely on the flash for lighting.
Try to avoid a back-lit situation because you will either appear under exposed or it will try to fire that flash.
If you're indoors, the most flattering lighting to show off a guys face, IMO, is to try to setup the 2 or 3 point light scheme. The trick is to get one or two sources coming from the side or rear corners of the subject to bounce the light highlighting the edges. Then your second or third source is coming from one of the front corners... creating opposing light sources. Sometimes you can find areas of the home with this type of scheme without moving a single light in your house, but you may have to play around a bit if you attempt this!
I do agree candid shots are best, but if you're doing this by yourself there isn't much you can do besides picking a great location with sufficient lighting and trying to look as natural as possible.