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Indeed, I have many times run a linux router by doing nothing but installing quagga, Net-SNMP, ipt_netflow, and I've got a lower end equivalent to some of the highest end commercial networking equipment.
Both OSPF and BGP provide the tools you need for policy based routing to various degrees, and quagga gives you that. The rest is just icing on the cake.
Ah, script tags... I agree with you completely. Programming languages merely describe a format electronic data format that can be read in by a computer program or piece of hardware affecting the state of the system in some way. They do not necessarily need to contain procedural instructions, and the definition of turing complete simply determines whether that particularly language is description enough to implement general purpose algorithms. Also, a lot of computer security issues come up from these non-TC programming languages being fed into a system and running instructions anyway.
As a theoretical example, someone's web server delivers a malicious image file that crashes the client image codec library and fools it into running code contains elsewhere in the malicious file. Doesn't matter whether that image was designed to contain procedural instructions or not if someone can fool the parser to run those instructions anyway.
I agree that installing a proper data infrastructure in a home is key for proper nerding out, and you have a lot of options to go over.
If you want to go for broke, put a 2" wall mount telecom rack somewhere near ground level (basements and storage closets are perfect for this) to keep noise in the system to a minimum. Go with cat5e or better for data, cat3 or better (cat5 or better works, but is usually more expensive per ft.) for telephone lines, and RG6 or RG59 (RG6 is lower loss, but more expensive and harder to work with, but you're laying down permanent lines) if you want a cable connection. Have a dedicated 20A breaker circuit run to power the installation and a rack level UPS and you're set to run in power outage and brownout situations.
There is a strong interest in 'cutting the cord' with cable, so you may be able to save on the coax and just not bother. The telephone lines can still be used with a voip box to give you access to the telcos with regular equipment, or you can use something more exotic like 802.11 or some enterprise level VoiP equipment. I'm sure you can keep going further and further along until you've punched all the tickets on your nerd card that you want to.