I use the fine point permanent Sharpie markers but I just write on them up by the stem/core - the part I'd be cutting out anyway. Usually a couple of initials or 3-4 letters is all I need.

Dave

makes sense...

I do the same as Dave - Sharpie up near the stem.

I only grow 3-5 plants every year, so I plant them in alphabetical order.

I think Dave's method is the best. I also use sharpie, from time to time , mostly when I want to take a picture to file/post.