Is there a way to sync my personal files to my Nook Color & G2 phone?
I don't believe that functionality works yet.  I have tried to sideload PDFs and plain .txt files and they don't register in "My Library" or under "My Files" and obviously they don't sync between my devices.  I also can't find a web interface for loading non-nook files.  

I did a little searching around a couple months ago and I found a few unsubstantiated forum posts that claim that it's planned functionality but the Android app currently only supports sideloaded ePub files.  


  If not, any ideas how I could
  accomplish this (other than doing it
  manually which I currently do)?


I'd say your best bet right now is to do this outside the Nook app.  Sideload (or wait till Jan for the Market) a PDF reader and Dropbox or SugarSync onto your Nook Color to keep your PDFs synced and accessable.

*For full disclosure: those Dropbox and SugarSync links are my referral links so if you don't already have them and you use those links both you and I get some free extra storage ;o)