Getopt::Long leaves any unknown data that it finds in @ARGV alone. So you could process whatever's left in @ARGV yourself after sending it through GetOptions(): 
my($help,$backup,$upd_sybase,$silent);
GetOptions('help|h!'    => \$help,
           'b!'         => \$backup,
           'u!'         => \$upd_sybase,
           's!'         => \$silent);

# assuming it's always key1 value1 key2 value2 in argument list
my %other_args = @ARGV;

# if your arguments are positional, do this:
# my($server,$password) = @ARGV;

# called like this: ./foo --silent server bar password blah
# yields:
# $silent == 1
# $other_args{server} eq "bar";
# $other_args{password} eq "blah";

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Update: Added an example for positional arguments since the OP seemed to maybe have wanted that --Brian

In reply to Re: Mixing command line arguments by bpphillips
in thread Mixing command line arguments by Anonymous Monk

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