Audio Systems: Home/Prof audio system, home stereo system, digital to analog converter

I will be replacing my hi-end home stereo system soon. It is past its prime. I am just getting into MP3, or better yet, FLAC. I am trying to decide what I need or what is available.
I want to be able to store MP3 or FLAC files on a system that can power "real" speakers. Everything that I see online, is iPod, and a little iPod dock station with little tiny speakers. I want a real remote to traverse music and play on at least decent speakers with a decent receiver (amp/pre-amp).Onkyo Polk.

Links to articles would be fine...
Computer/tech savvy, but nothing I can find to do what I need.

An iPod wont really store FLAC files even though you can archive your master tracks in FLAC. You would then convert them to at least 256 VBR mp3's. Apple even has their own lossless compression format which is not as good as wma9. Unfortunately Apple will convert any wma files before it goes on the computer.

As far as a sound system there are many important elements in the reproduction of digital sound. First there is the DAC (Digital to Analog Converter). The one that is built into an iPod is obviously not a high quality device. The best sound reproduction will be achieved using an external DAC to your computer.  There are professional and consumer DAC's. The consumer DAC will generally connect to your computer using a USB or an Ethernet cable. One divice you might want to look into is made by Logitech. It is called a Squeezebox or Squeeze Center. The device will automatically find all of your computer music files (even FLAC).

Next would be to choose a good quality receiver. Most major brands from Technics to Onkyo make good receivers. As far as speakers there are a plethora of quality speakers: Polk, Pioneer, Tannoy, Bose, etc. You need to decide if you want recessed or surface mount. The addition of a subwoofer will also enhance your listening experience.