For years I've used Jagwire's spiral wound brake housing and "compressionless" shift housing. I buy them in 25' or 30' rolls and they provide years worth of bike overhauls. The spiral wound brake housing has been more than satisfactory with caliper rim brakes and the shift housing allows very accurate shifting.

I recently built up a Surly Midnight special with TRP mechanical disc brakes and, at TRP's recommendation, I used Jagwire "compressionless" Pro brake housing. I don't know if it is essential but it does give a very solid and predictable brake feel.

As to inner wires, I use both Shimano and Jagwire with equally good results.