Uses of whole genome comparison?

[Charade]

Hello,

I'm a computer programmer trying to understand a few concepts in
molecular biology. Since I have no experience in this area, I am
looking for some help.

What tools are available for whole genome comparison? Is this useful?
Is the sequence to sequence comparison for whole genomes, using the
smith-waterman algorithm to get the optimum score a useful tool?

What organism genomes would be interesting to compare? I'm looking to
create a tool to compare genomes in the 1-10 million base pairs
region. I will of course only be calculating the optimum score and not
the alignment.

Once the score for the annotated sequences are calculated, what is the
best method of visualization? I was planning to plot the scores in a
grayscale image, with darker regions representing homologous
sequences.

Thanks for any input.
Charade.