First of all, if you use Microsoft Office Word, you can use digital signatures features. You would first put your digital signature, email document to a customer, your customer puts their digital signature and emails a copy of the document back to you. This is as good as signing on paper. Follow the link below for a step by step guide how to do this in Office 2003 and Office 2007:
http://www.microsoft.com/downloads/details.aspx?FamilyId=79d06e72-4b45-4669-9eac-0eca5821e8ff&displaylang=en
If you cannot use digital signatures in Word, then there are two ways in my mind.
If this is a high business impact document (contract, statement of work, payment bill), I would still use the standard old way when my customer prints the electronic version, signs it, scans it and emails back to me. Check with your legal department on that.
For low business impact documents (specifications, plan of actions, etc), I usually have two parts of my document that I use for that:
a) An OARP table on the first page. I identify all approvers and put "Signed Off Date" column to track a date when an approver signs off on the document.
b) A table to track changes and major events at the end of the document. If we signs off, I will add a row with date, description ( signed off in a meeting on in ) and a name.
And I save a copy of an email or meeting notes in the same documentation repository as where the document is.