Thats a great idea which had not occured to me. I was not in fact using precompiled regexps, but when I switched to them it seemed to slow down my code (from 25-30 secs on my test data set to 3+ minutes). I'll give the search reversal a try and let you know how it turns out. Updated code using precompiled regex:

my %htable_re;   

#reading in small file  
while($cur_line=<size_log>)  
{     
    my @command=split(/;;;+/,$cur_line);     
    $htable_re{$command[0]}=qr/\b($command[0])\b/i   
    #parse remainder of line...  
}     

#pattern match against big file  
while(<fh_log>)  
{
     foreach $key (keys %htable_re)
     {     
        if(/$htable_re{$key}/ ) #If this query contains reference to t
+his table     
        {
            $table_stats{$key}++; #count up how many times this table 
+is referenced.
            $table_refs++;     
        }    
    } 
}
[download]