I used to use Excel to keep totals (as a summary) and then Word to do the actual invoicing - man that was long winded!
I then discovered FreshBooks, but after about 5 months of use found it hard to justify the cost of keeping it going. So I am now using
http://www.billfor.it as I was invited to their beta site. The invoicing and quotation side of things is really good and easy to use. The invoices can be fully customised too - although the HTML editor is a little hard to get to grips with
Apparently the site is launching on 1st Nov - I've been using for about 2 months in beta and pretty confident in it as have had no issues. To be honest - anything is better than Excel and Word for doing the invoicing!