It depends on how deep they are. If they are very shallow, they can be rubbed out with any number of running compounds and then buffed with a good polish/wax. You could also wet sand them with super fine paper (600 or higher grit) and then buff out the area as well. I prefer the rubbing compound method myself, but either will work. Again, all this depends on how deep the scratch actually penetrated the gelcoat.

This is what works well for me and worth the expense. Buy from West Marine or Boat World, 3M's marine rubbing compound (10-15$), finesse-it polishing compound (20-25$), 3M's 6 inch polishing pad (20$) which attaches to your electric drill. Also buy a 4 inch compounding pad and arbor kit from Lowes/Home depot (5.00$)which also works with your drill. Obviously use the compounding pad with the compound first, follwed-up with the finesse-it with the polishing pad. Then, wax. Clean up from flying compound is easier if you throw a sheet over sorrounding area and don't be afraid to compound hard enough to generate some heat. The finesse-it will remove any swirl marks and make the area as shiny as new.