> However, when the
> number of links that it searches gets too large ie. 1000 
or
> more, httrack slows to a crawl and is really slow.

Weird - the internal hashtables should be able to handle 
thousands of links without problems. But if all files are 
stored in a single directory - it might be a filesystem 
slowdown ?
What is the OS and filesystem type you are using ? 
(Windows ? FAT32 ?)