Hi - what is the most reliable way to purchase tickets to the museums in Florence and Rome?

I found these on Rick Steves website. Anyone used these? Were there problems or smooth sailing?

www.weekendafirenze.com
www.b-ticket.com/b-ticket/Uffizi

http://biglietteriamusei.vatican.va/musei/tickets.

Your question is a bit obscure; reliable as in ability to get you IN the museum...? or ability to minimize waiting time to access museum?

There are hundreds of museums in Rome, same with Florence. I think you need to first downselect from those hundreds to the ones you MUST see. I see you already sort of started to do this with Vatican Museums and Galleria Uffizi. I used the site you listed for a Vatican Tour and it worked fine.

What time of the year are you going? Waiting tickets lines are reduced dramatically in off-season months.

You might want to add this as the Borghese requires advance reservation:
http://www.ticketeria.it/ticketeria/borghese-eng.asp

BTW, most museums do not require advance reservations or tickets.
Of course there are exceptions such as the Uffizi, Accademia, Borghese, where it is helpful or required.

The official website for the state museums of Florence is:
http://www.polomuseale.firenze.it/english/Default.asp?
You can purchase tickets through the website for multiple musuems and when you click on book ticket online it will roll over to the b-ticket.com website.

The official Vatican Museums website is:
http://mv.vatican.va/3_EN/pages/MV_Home.html
It rolls over to: http://biglietteriamusei.vatican.va/...ets/index.html

You might want to consider the Roma Pass for other museums in Rome (including Borghese).
http://www.romapass.it/p.aspx?l=en&tid=2

There is much to be said for phoning museums in Florence to prebook your tickets at +31 055 294883. Open during museum opening hours, English spoken, one number for all public museums. No prepayment required, and if you turn up at the museum and the line is quite short, you have the option of just getting in the normal way and saving 4 euro reservation fee (per person) when picking up reserved tickets. If you book online, you have to pay there and then, so this option isn't open to you. Also phone booking has a lot more free slots than online (e.g. has no morning slots).
As for the Vatican, the line is almost always long, so 4 euro is a small price to pay for jumping the queue.