We use FogBugz, Greasemonkey, Asterisk, and Snappy to manage Fog Creek's customer emails, phone calls, and faxes. It's great for customer service, and for generally managing communication. Here are some details.
There's a comprehensive email system in FogBugz that both allows email into the system and sends responses back out, tracking emails using case numbers in their subject lines. We use "FC" as our unique prefix.
Sometimes people want to track their customers explicitly with Clients, Areas, or something like that. That could make sense if you only have a few clients. You can change the name of either the Computer or Version fields to whatever suits your needs, such as "Customer ID." Also, as long as you're using SQL Server or MySQL for your database, you can use FogBugz's full-text search, which includes email addresses and case comments, whenever you're looking for something.
We have lots of customers, so instead of dedicating an Area or the like to each customer, we use search to track and find cases dealing with a particular customer. We also use "see also from this correspondent" and "see also from correspondents at this domain name." Those links appear automatically in a FogBugz case where email's been sent or received.
We also use a Greasemonkey script with our Firefox web browsers to automatically pull relevant customer information from our web shop's DB onto our FogBugz screens. The key for us is the Correspondent email address, but you could use a customer ID number.
We use FogBugz to track phone calls as well as emails. Whenever I receive a phone call for support and I don't have an immediate answer, I click "New Case" in FogBugz and start entering details. Or I'll use FogBugz email to send a sales prospect information they request on the phone, and set a due date to remind me to ping them in a few weeks.
Our phones run on the open source Asterisk switchboard software, and we set it to turn voicemail into sound files and email it into FogBugz. That way, each message a customer leaves for us turns into a FogBugz case. We've set up separate email addresses and FogBugz mailboxes for sales and support messages, so FogBugz learned quickly which Inbox Area to put those cases in. Incidentally, we also receive personal voicemails as emailed sound files, which I much prefer.
We do the same thing with faxes, using Snappy Fax Network Server. Snappy receives each fax, turns it into a TIFF, and sends an email into FogBugz with the TIFF as an attachment. Again, FogBugz learned quickly that those emails belonged in the Fax Area.
Our online shop sends special email into FogBugz if there's an error or a suspect charge to approve. Our online contact form feeds into FogBugz, as does recruiting email. And of course we use BugzScout to automatically turn crash reports from the field into cases. It's our centralized repository of knowledge, it's easy to extend, and it's just one database to back up.