I bought my garden markers from Everlast Label Company, and couldn't have been more happy with the price and service I received from them. I was thrilled! I used the P-touch labeler to make the labels, and they have held up really well. I used the ones for extreme weather, and they haven't faded at all in three years.
For seedlings, I use mini-blinds, which I write on with a pencil. The pencil is as clear as can be after 2 years. I do have other plants that I've marked with the mini-blinds and pencil, and after 4 years, the writing is still as clear as it was the day I wrote it.
I did use some of those paint pens, and had horrible results. Totally faded out after a year and I can't read anything!