The sun never sets on the British Empire!
...because you can't trust an Englishman in the dark
Best method of storing and searching old email? Gmail. It can import from pop and imap so you can point it at your other inboxes and let it get on with it.You can upload from other mail clients to Google's imap server. Obviously it's amazing at searching through the archives.
Best method if you're concerned about Gmail's privacy? I'm still working on that one.
The solution is Google Apps for your own domain. $5 a month per user, 25Gb space, IMAP, no advertising (which is where most of the privacy issues arise), and most importantly, no lock-in as you can switch your email to a different provider at any time without changing email address. As you said, Gmail is by far the best for searching old email. I haven't run an email server for years.
So now you can't search for the UK city of Scunthorpe, and some people with text strings in their name which some Google droid has added to their unaccountable blacklist have also simply disappeared from the new regular search results.
Google Search is becoming like Apple's products - sanitized according to respect the arbitrary moral values of an up-tight, unaccountable elite.
All kidding aside anybody with the skills and resources can now take over 1.3 and keep updating it. You can not really EOL a FOSS program if anybody wants to keep it alive.
OpenBSD's forked version of Apache 1.3.29 already fulfills this role.
"There is nothing new under the sun, but there are lots of old things we don't know yet." -Ambrose Bierce