After consulting my wise elders, I offer the following explanation:

<dledford> linville: If I recall correctly, the issue is that
basically in 2.4, a standard driver loads, it searches the PCI device
list for possible device matches and grabs the ones it wants.  As a
result, devices are usually found in PCI device list order.
<dledford> linville: For 2.6, pretty much all the drivers are switched
over to using the PCI regristration mechanism that enables hotplug. 
But, that means the driver doesn't search for devices any more, it
registers a table with the PCI layer and the PCI layer then calls it
when a device matching an entry in the table shows up.
<dledford> linville: Probably for purely no reason other than "it made
sense to sort things this way", the PCI layer may be looping over the
PCI device list, checking for one entry in the table at a time or
something like that, which could result in the detection order
changing between 2.4 and 2.6.

The ordering is fundamentally cosmetic.  If it truly bothers you, you
can change it like this:

   cd /etc/sysconfig/network-scripts
   mv ifcfg-eth0 $$
   mv ifcfg-eth1 ifcfg-eth0
   mv $$ ifcfg-eth1
   vi ifcfg-eth[01] # change DEVICE= lines to match new filenames

Then, reboot (or `service network restart` might work)...