Profit,
I don't have omniweb, so I don't know exactly how it reformats html files. However, this sort of task is exactly what perl was made for, so I would make a perl script to reformat your files. (Of course, I probably would try to combine these perl programs so you can simply read unformatted html files..)
Here's a perl script you could use as a starting point. Good luck!
<font face = "courier">#!/usr/bin/perl
# reformats html files -- puts newlines after each <br> and
# before and after each <p>. Usage: "reformat.pl <html files>"
foreach $file (@ARGV)
{
open(IN, $file);
open(OUT,">$file.reformatted");
foreach $line (<IN>

{
chomp($line);
$line =~ s/<p>/\n<p>\n/g;
$line =~ s/<br>/<br>\n/g;
print OUT "$line";
}
print OUT "\n";
#`mv $file.reformatted $file`;
}</font>
--Juggle5