You need to look a bit closer to see the difference.
APU uses cheaper realtek NIC and soekris uses Intel's.
Soekris gives Intel QuickAssist to help encryption (VPN etc.). And soekris is showing up a new model later this year: http://soekris.com/products/net6801.html
But PC-engines boards are nice for their price. I'm considering to get one at home. That or spend a bit more on soekris box/
The NIC used is also important if you need the router to do PPPoE. Most Intel ones will support jumbo frames which can let you still get 1500 byte packets to the ISP.
damn. you people are like audiophiles for network. ...is there a name for that already?
those two boards have more CPU power than my home theater PC... which crunches 720p video all day long without a decent GPU.
This is nothing like the absurdities of the audiophile community. Routing traffic just isn't as trivial as you think it is, and going with cheap NICs that are missing important features and have lower-quality drivers will produce measurable and significant differences in objective benchmarks. If you have something like a 100Mbps cable connection, you can't use just any off-the-shelf hardware and expect to solve any problems in software.
Thats what an audiophile would say
;)
It's also what the IETF says. Don't belittle those who are trying to fix the problems you're frustrated with but can't be bothered to understand.
[0] http://www.pcengines.ch/apu1d4.htm