Best Tri or road bike for $500 - $1,000?

My thoughts for you are:

1. Buy the bike shop; not the bike.  You would be better off finding a good bike shop that can fit you into the right bike than concentrating on any one particular bike or brand of bike that I or anyone else could suggest.
   
2. Your price range is better suited to an entry-level road bike than a Tri-specific bike.
3. You are at a good time of the year to take advantage of '08 closeouts so you might be able to buy a more expensive bike that has come down to your price range.  Again - your local bike shops are a good place to start.
4. Consider buying used or new through the Internet only if you already know what you want to buy and what measurements fit you best. 
5. Finally, I assume you already have some gear, but my advice is to not forget some of the nice-to-haves for you bike (some would say "essential" ) like shoes and clipless pedals.
   

 As far as your question about shifting, many road bikes have Shimano STI shifters like Sora, 105 and up that allow you to shift from the drops.

I ended up getting a Nemesis from Bikesdirect.com  for $995 w/free shipping

 Though I really don't like the aero bar, the only things I added were the bottle cages/bottle for hydration, a seat bag and spare items in case of road flats.  I've been happy thus far.

 I found that the frame is the same as the Fuji Aloha and another frame from Giant.

I bought this bike knowing that I did not want to by a cheaper bike and then spend much more $$$ on upgrades.