I have a Waterford (made in Wisconsin, not Italy, sorry!). They are all custom. They are very well known and have a very good reputation.
I bought mine used, so can't discuss custom fit, etc. Waterford has great customer support, they've answered questions for me about my 10 year old "new" bike. They have a message board for Waterford owners, too. www.waterfordbikes.com

Several women on here have Rivendell bikes. They have a production line made in Japan and a custom line made in the US. I think they use Waterford tubing. I've seen quite a few custom frame sites proudly declare they use Waterford tubing, so that's something to keep an eye out for. www.rivbike.com

My boss has a custom ti Seven. She researches things down to the last detail.

So, those are the three I know anything about more than just the web: Waterford, Rivendell, Seven.