1) What happens to my ability to get into websites Passwordmaker has protected - if I have a hard drive failure and have to reinstall from scratch? I know that a backuped hard drive is a good thing, but previous experience has taught me that this does not always work as it should.
The only things that you need to be able to reproduce your passwords are:
a - your Master Password, and
b - the Settings used to create the password.
So, if you changed the PM settings to something other than the defaults (which is highly recommended for security), you will need to be able to reproduce these if you ever needed to reinstall PM.
The easiest thing to do is keep a backup of the PM RDF file, whcih is where the Settings are stored.
2) I use several computers throughout the day, in several locations. It sounds like the only way to access protected websites is to email myself a file and download it on each computer. Since some of the computers are public access ones, this raises security concerns for me.
Nothing to worry about, really... if it were me, I'd keep my RDF file on a secure FTP server so I could access it from wherever, then you could install PM, copy your RDF file over, use it, then delete the RDF file before you leave.
Alternatively, you could use the online version, although it doesn't support Custom Accounts, and would require you to know what Settings you used for each Account.
There is a plan to integrate synchronization between the online version and yours, but that is not available yet.
3) Is there some way to view all the sites that are protected? not just the special sites (accounts?) but every website ever protected...and a list of passwords?
No - PM doesn't store passwords anywhere (with the exception of the Master Password, if you tell it to). Account Passwords are always generated on the fly - nothing ever stored either in memory or on disk.
I'm thinking of certain websites that are visited very infrequently, so much so that I may even forget that they are protected with PWM rather than my normal password system
Again, all you'd need to be able to do is remember the Master Password used, and the Settings - and as long as you didn't lose your RDF file and didn't use different Master Passwords, that should be easy.
Personally, I use multiple Master Passwords, determined by what 'hat' I'm wearing - ie, a different Paster Password for each Client I work with, and one for my Personal Accounts.