You can use lots of programs to generate a simple invoice, word & excel for instance, if you use open office you can generate the invoice as a PDF file with clickable links for payment options.
You can also make an invoice using HTML, if you're comfortable with that.
Paperless billing is becoming the norm, as long as you have, or can print out a hard copy if required, & you use some sort of invoice numbering system you should be OK.
I save all my email invoices from eBid & statements from Pppay ect as PDF files, there are a few free PDF Converters out there http://www.primopdf.com/ is the one I use. It installs as if it's an extra printer. So if you open the email invoice, or the webpage with the statement on it, & choose print, instead of using your physical printer you choose primo, it then saves the invoice or statement as a pdf file, ready to print IF the revenue require it.
I keep all mine account stuff together, & a backup copy on a CD, my accountant is more than happy with this, he doesn't require hardcopy of everything, that way if the revenue want more info you can hand over the CD & they can waste their ink & paper printing it out.