> 
> A couple of years ago a friend of mine bought me a Mustek parallel port
> scanner.

Some friend!  ;-)  Locking you into windows!  Boo! ;-)

...
> When I scanned a picture, straight lines were pixilated & weird. Overall
> quality was poor.
...
> Anybody know why running a VMWare Win98 and scanning would produce somewhat
> corrupted results rather than running it in native mode?

Probably your scanner is dumber than I'd have expected and uses the parallel
port for timing as well as data return!  If the scanner has critical timing
requirements that cannot be met by vmware you can get funky results.

BTW - how fast is your machine?  How much memory?

> Could this apply to other things as well, such as data on a hard drive?

No, disk drives don't (USUALLY!) start writing until all the data is
in the buffer, and timing is thus not critical...

BTW - scsi scanners can be had for as low as $70 street price....
(I bought one recently for $60, I think).  (Beware - Agfa's 
support stinks!  I strongly recommend against their scanners 
because of their lousy support methodology -
it cost me more to get them to replace the scanner for free 
than it would have if I'd just trashed it and bought a new one!)
(I had to buy a new bulb to prove to them that the bulb was
not the problem.  THEN, $45 later, they said - oh, shoot, its
a main board problem - we'll ship you a new one...  No mention
of letting me return the completely UN-NEEDED cold-cathod 
bulb - anybody need one for their agfa scanner???)

Yikes, that really diverged.  Back to the point -

I'd suggest looking into scsi scanners, or check SANE to
see if they support any usb scanners yet....