bungrider -
If the choice were between XYZ desktop and a shuttle-based config or someone had a uniquely compelling need to routinely lug around a fairly ruggedized desktop equivalent, those are all key differentiating factors.
But laptops have made a big leap in the last year or so and 99.99% of the people looking at a laptop aren't likely to exceed the capacity of a 2GHz Pentium 4 with up to 80 GB of disk, up to 1GB of RAM, integral DVD/CD, AGP video, Yamaha 3D sound system, firewire, dual USB, 100 Mb network, and Wi-Fi capabilities.
The factors that you mentioned that could dictate otherwise though are valid -
Running multiple monitors - an exceedingly rare requirement for a portable machine, but for those unique instances you can't do with a laptop (at least not without using a docking device)
Needing more disk capacity - also fairly rare for a portable machine to need more than 80 Gig but it might be easier to carry one of the latest generation external high capacity storage devices if you do than lug around the bulkier config
SCSI devices - can't think of too many (if any) situations that mandate SCSI (especially for portable use) but if there is then you either have to connect the SCSI devices to the laptop externally or go with something like the Shuttle config
Faster - you definitely can load up something like the Shuttle with a 3+ GHz P4, but it's hard to imagine too many applications (especially portable ones) that need more than the laptop's available 2GHz P4 - heck, you can do video editing on one of these laptops
Cheaper RAM and storage upgrade - absolutely true, but how many portable uses need to upgrade beyond 1GB of RAM and 80 GB disk?
PCI/AGP - the laptop video is already AGP, but if you absolutely need PCI expansion, then the laptop can't do it without a docking station - you have to go with PCM or USB expansion on the laptop
Better audio - if you output the audio output of the laptop's integral 3D sound system to a good speaker system will anyone be able to tell the difference? I've seen several commercial dance floors, traveling DJs, and entertainment facilities use this type laptop as their whole digital music (and even video) center
3 Firewire and 4 USBs - it's hard to imagine a portable application needing that many connected firewire and USB devices, but if there is, then the laptop couldn't do it - it can only handle 1 firewire and 2 USBs (unless you use a USB extender anyway)
Cheaper - probably, although except for the high-end sub-notebooks or tablets that are pretty pricey, I believe that the notebooks in question are around $1100-1300 and they're only a small fraction of the weight and bulk of the alternative (so you've got to factor in how much that's worth to you).