This is an excellent topic for discussion and I too am interested to hear others share about their experience.
I'm just a small-time hybridizer with very limited growing space so I've adapted to what works best for ME. Like Debra, most of my beds have other perennials inter-mixed with my daylilies so I have some color throughout the whole growing season. I'll focus my comments on the one bed I created just for my daylily seedlings 7 years ago.
I made this raised seedling bed 6' x 18' long; 6" between each seedling, 6" between each row, every third row I left 12" so I could step in and weed when I needed to. This allowed for 243 seedlings. At the end of every 2nd year, I culled what I needed to and moved the rest of the keepers and those that had not bloomed yet to other areas so I could start this bed over again. This is when my seedlings are designated inventory numbers beside the abbreviated cross.
That first year I used the 7-8" white plastic markers and wrote the full cross on them with a black permanent Sharpie pen, one marker at the beginning of each cross. By the end of that summer, many of the labels began to fade to the point of illegibility. Thankfully, I caught these before they faded completely and re-wrote them. Unfortunately, over a dozen ended up laying in the yard somewhere else or disappeared completely. YIKES!
I learned a lot from that first full season (or rather, the squirrels in my neighborhood taught me a lot). I have not used these white plastic markers since that first year, not only because of the written crosses fading, but mostly because of the darned squirrels make a game of pulling them up and carrying them off somewhere. (Becki-0, Squirrels-1) Needless to say, I am on a first name basis with most of the squirrels around here. There is @#!!*&, +^%&!! and %&$!!, well, you get the picture.
Anyway, since that first year, I decided I needed a more productive and fool-proof (or rather squirrel-proof) way of labeling my daylilies. The second season and thereafter, I have used the 11" metal plant markers and the Dymo labeling system (because it was the least expensive I could find). I can push these 11" metal markers twice as far in the ground as I could the plastic ones, they don't break and most importantly, for some reason, the squirrels completely leave them alone. (Becki-1, Squirrels-1)
The plastic labels (I use the white background with black lettering) last for a solid 3 years before any begin to show any signs of fading (at least in MY garden), so I replace the labels every third year, just as a preventative measure.
But for ME, the most important thing I do is to make a hand-drawn map at the end of each season of each of my seedlings bed. Because I move some plants in and out each year (cull the uglies and sub-par, add new purchases)its crucial that I do this.
On these maps, I draw out the shape of the bed and make a small circle where a plant is and give that circle a number. Then I make a corresponding list of the plants and crosses on a sheet of notebook paper that I staple to the back of each map. I slip these into a clear plastic report cover and keep these in a cheap 3 ring notebook that I keep for my seedlings. I double check these every fall and make any necessary changes. This way I have an updated paper copy as a backup just in case my plant markers get moved. (Becki-2, Squirrels-1)