I applied to this. It was a form online, and I paid €50.99 at the time. (€50 for the application fee and a €0.99 charge to cover the cost of paying with a Visa or MasterCard.) It took about twice as long as they promised with my application (although this was just after they'd started online applications), but with a little nudging by email, the package (card, reader, PIN numbers, etc) arrived at the Estonian embassy in London. A signature and some fingerprints, and they handed over the package.
I feel they could have been a little more transparent and clear about what stage my application was at, but overall it was fairly easy.
You don't actually have to go to Estonia to collect the card or do any of the processing in person there anymore. It can be done all online and everything delivered and finalized at your local Estonian embassy or consulate. When the program first started, to apply you had to make a physical appearance in Estonia. You still do to open up a bank account -- for now.
The software does work on Ubuntu. There's poor or no support for other distros IIRC.
I've yet to incorporate or actually use it for any practical purpose, but I expect to in the coming month or so. Estonia is doing some really cool things and it seems to be a decent jurisdiction to run a location-independent business from. I've still got a lot of experience to gain though.