[[NSUserDefaults standardUserDefaults] setObject:yourMutableArray forKey:@"Key"];
A mutable array can be stored since it is a subclass of NSArray.
To get the value as an NSMutableArray:
NSMutableArray *array = [NSMutableArray arrayWithArray:[[NSUserDefaults standardUserDefaults] objectForKey:@"Key"]];
or
NSMutableArray *array = [[[NSUserDefaults standardUserDefaults] objectForKey:@"Key"] mutableCopy];