[MatrixDweller]

The only way to really future proof is to run conduit or get good at fishing wire. Besides that it wold be buying the most cutting edge cables/connections that are currently on the market. That would mean HDMI 1.3b certified cables, Cat6 network cable, 12 gauge speaker wire, triple shielded RG59 and anything else you might fancy.

A HDMI 1.3 certified cable should be able to run 1080p its full length. They do make them in 25ft lengths.

For networking you would be best to get a DSL/Cable decent router and make a communications closet. Your DSL or Cable internet connection would be there hooked directly to the DSL/Cable router. You could use a Star Topology (run everything from the central point to it's end point). Or you could use multiple routers if you plan on having multiple network connections in multiple rooms. In that case you just need to feed one CAT6 line to each distribution point. The price of CAT6 is only marginally higher than CAT5e so don't skimp now.

You could also go wireless and use a wireless N Cable/DSL router and wireless access points hardwired to your network devices. Wireless isn't as secure and reliable as wired, but can be a lot simpler.

For speaker cable runs I'd use 14 gauge minimum CL2 rated wire. If you can afford 12 gauge go with that especially for long runs.

I would run coaxial digital audio using RG59 cable. It's a lot stiffer and will be easier to fish through your walls.

As for retro conduit, if the drywall is up you can really only do conduit parallel to your floor joists and studs and or vertically from floor to floor (or though and attic or crawlspace). If going through an attic or crawlspace make sure to properly seal and insulate the opening you created. You can run cable through baseboard raceways, crown molding or external conduit also.