512 kB Or 1 MB 2nd Level Cache
Motherboards with 1 MB of L2 cache should be preferred because of two important benefits: First the system performance rises a bit, and second the larger cacheable area helps to keep the high system performance you are used to also with larger amounts of main memory.
I also ran the benchmarks you saw above on a FIC VA-503+ and 1 MB L2 cache. The performance loss you will have to expect when using slower clocked memory (66 MHz instead of 100 MHz) is smaller in deed. The business performance measured with Winstone 98 does only decrease by 2% instead of 3% with only 512 kB, Quake II runs about 10% slower instead of former 16% and Incoming becomes 1.2% slower (about 2% at 512 kB). The results with EDO DRAM show roughly the same relation.
This shows very well the advantage of having more cache: A larger L2 cache does not only improve the system performance, but also moderates the negative performance impacts when using older memory or SDRAM which doesn't run at 100 MHz.