You weren't specific about how you'd like the images combined. I'll let you play with the different imagemagick options. Here's some code to get you started.

#!/usr/bin/perl
use warnings;
use strict;
use Image::Magick;

my $image1=new Image::Magick;
$image1->Read("dir1/1.gif");
my $image2=new Image::Magick;
$image2->Read("dir1/2.gif");
$image1->Composite(image=>$image2,compose=>'plus');
$image1->Write("dir1.psd");
[download]

However, check out ImageMagick http://www.imagemagick.org/ for some command-line tools and even a set of Perl bindings to let you script a solution.

Further, I recommend you work with portable image formats, not .PSD files. Sure, load the file into Photoshop if you must, but consider TIFF or PNG or some other format if possible for your application. You weren't clear if you wanted to import images as layers, but PSD isn't the only format which can help you there.

I downloaded imageMagick and have it working to append images together. This is good, but I do want to import the images as separate layers, so that they are independent and I can rearrange them. Do you know how to do this? I have checked the user guide, but it doesn't seem to tell how to do this.
Thanks for your help, Jon

I thought it would be easy, but I'm having trouble with layers too. I did get it to work saving the output as a gif, so I wonder if I don't have all the support libraries to write multi-layer psds.

#!/usr/bin/perl
use warnings;
use strict;
use Image::Magick;

my $image1=new Image::Magick;
$image1->Read("dir1/1.gif","dir1/2.gif");
$image1->Write("dir1.gif");
[download]

I'm opening this multi-layer-gif in gimp. I don't know if photoshop will open it the same way.

Update: .tif also works as a multi-layer file, at least you won't have to combine both images down to an 8 bit pallette.