I know Im late to the game, and that almost EVERYTHING that could be said has been said, I would however just like to add my 2 cents!
This move could go either way, Intel will provide the kind of performance and speed Apple wants to provide to their clients, but Apple is now part of a bigger cut through environment. We might think its good that Apple can now do a improved Power Mac every 60 days, but just imagine what Apple will have to do to get that done, and get their stock cleared before the next revision!
Looking at the pros Apple can save them and us a lot of money if they play this one smart. But ultimately I think apple will have the software sorted, it comes down to the hardware, so here is what I think apple should do:
1. Have Intel produce the Northbridge, that way Apple dont have to worry about the large amount of different socket types Intel has currently... they can let Intel do that. Apple also gets kick ass memory controllers and support for PCI express out of the way while reducing costs.
2. Apple should produce the Southbridge. By making their own Southbridge they can produce the hardware lock the platform will need. By restricting information about the exact hardware, like the SATA controller, Apple can make sure that the OS X only boots or at least detects the presence of one of their Southbridges and ensure that it wont boot on a stock dell. This way not only will someone have to emulate the rom but also provide accurate emulation of other undocumented devices such as the SATA, IDE, USB, Firewire (Intel doesnt do firewire btw), modem and whatever other device the chipset features. Using some sort of advanced identification method, no support for other boot devices and requiring apple only hardware to be present to even start the kernel will make hacking the platform rather difficult.
3. Apple needs to closely, but not completely adhere to the Intel motherboard form factors. If apple did a BTX motherboard everyone will simply install the board in their vanilla case or their AMD board in the G6 case. By changing the physical shape a little but keeping with other requirements like cooling placement and power supply specs apple can use stock power supplies and normal cooling designed for those cheap ass lamo dells.
4. Expansion devices. This in one place Apple can score big time. If Apple could use standard x86 based PCI express hardware, manufacturers will have the extra incentive to create drivers, as they can expand their market and use their existing hardware designs as is. This will be very much like USB, most USB devices work on the mac as well... unix driver and standards hardware and you have Mac support! Graphics is a bit of a grey area for me, Apple could also go standard but then Mac users will upgrade to the latest and greatest every time something new comes along, in turn possibly making support and controlling the platform for Apple harder. I would allow ATI and nVidia to use physical and electrically compatible designs but require some sort of advanced software identification, meaning that ATI would still have to produce a Mac version but it would simply entail a new bios. On the other hand if Apple could get ATI to do drivers like they do for windows all people would need to do is boot OS X in 256 colors, install the drivers and reboot into wonderful accelerated full color bliss... using cheap ass standard graphic cards.
I think Apple should push the new hardware out the door ASAP! Start with the laptops... skip the G5 powerbook and go for the G6, without using the hated intel inside sticker make it known: "we also use the pentuim M, we also have 8 hours battery life", then migrate the Power Mac and iMac, Apple needs to worry about their laptop line first, thats the thing suffering the most at this point. Use the dual core chips in the PowerMac, and the single core ones in the iMac, use the Celeron in the Mac mini and the eMac.
Thats my 2 cents.