> So, it doesn't seem to be just an Apache issue -- Apache 
> runs fine with other products.  It seems to be an issue 
> with the combination of WinHTTrack and the Apache 2.0 
> running on Linux.

I also use an Apache server (Apache/2.0.49 (Debian 
GNU/Linux)) to make tests with HTTrack on Linux (Linux 
2.6.5 on Debian SID) and I could not reproduce the issue.

Are the files dynamic / static ? Any errors in the logfile ?
Can you try the following:

1. Set Options / Flow Control / Uncheck: "Persistent 
connection (Keep-Alive)"

If the performances are still bad,
Set Options / Spider / Check: "Force OLD HTTP 1.0 requests"

But I really don't understand why it would took such a 
great time, and especially why combination with 
Apache/Linux/HTTrack!