The biggest reason the Pegasos gets a lower score than a Mac is because MacOnLinux does not use 2D/3D acceleration. So do not judge the Pegasos as slow simply because we get a lower score than say a 1GHz eMac.
MacOnLinux adds some overhead to memory and CPU access as well, although the CPU-benchmarks should be fairly accurate to actual performance.
CPU, memory and harddrive performance should be the three best areas to check when comparing to other systems on the XBench site.
Because of the memory bug I can only access 256MB of my total of 512MB. I only set aside 128MB for MOL to avoid swapping in Linux.
My Pegasos II/G4 with 512MB of DDR266, 60GB UDMA100, one Sony DVD and one Sony 52x CDRW and a Radeon 9100 128MB cost about as much as an eMac 1GHz/G4 with 512MB, 80GB HDD and Radeon 7500 does in Sweden.
