My ESXi 4.1 crashes when I boot a virtual machine that has a PCI passthrough device. The vm has two PCI devices that are passed through to it. Booting with the first card works fine. As soon as the second card is added ESXi crashes.
Try one card then remove and try the other. See whether you can change the interrupts the cards use. Disable any unused onboard components like serial and parallel ports to free interrupts.
What sort of cards are you adding?
The crash also happens if the only the second card is inserted (first card removed). BIOS doesn't support manual assignment of IRQs (or I wasn't able to find the setting). Disabling all unused onboard devices didn't help either (unfortunately).
It's the card described in this thread:
http://communities.vmware.com/message/1686544#1686544
What's new: I found a tool with which I could tell the pci card to be a network card (so it was no longer only a bridge). With this trick the card was available for passthrough (and crash too )