My own perception would be also to rank Sequoia, Kleiner Perkins, and Benchmark as top 3, but to put KP half-a-step above the other two, and Sequoia marginally above Benchmark. Especiaually during the last bubble KP really had a reputation of a golden touch in SV, and their startups had an advantage when recruiting. I suspect that people PG surveyed formed their brand perception over longer time than I have.

I think the ycombinator ranking is focused on internet companies. What about the VCs that invest in (yes I know yuck) enterprise software?

I think they're basically the same firms.