I have the same problem using the pens. My writing/printing isn't the greatest and sometimes there are little blobs of ink at the end of a word. Overall the results using pens have been less than desirable and after putting so much effort into the quilt itself and trying to make it look "professional", the pens made the label look second rate.
I have been using machine embroidery for most of my labels. They look great but since I don't have an embroidery machine I have to pay my LQS to make them for me.
*However, a friend suggested that I try using "Bubble Jet Set 2000 for Hewlitt-Packard Printers". Our LQS has it for sale. It allows you to print from your computer onto 100% cotton fabric and it can be used with all ink jet and bubble jet printers. Some quilters use it to transfer photos from their computers to fabric. With this product you can make up a label on your computer using whatever font and colour that you want and you could even add a photo if desired. My friend has tried it and said it is easy and the results are very good - I haven't tried this yet but I am definitely going to in the near future.