I tattoo every rabbit when it is weaned. I use a clamp style device. You have to clamp down hard to ensure all characters penetrate / pierce the skin and then apply human-grade tattoo ink. The stuff they sell at the rabbit supply places does not work as well.
I've seen folks use the pens. It sure looks nice when they're done. (But I don't think they'll come tattoo my rabbits for me.) I've gone with the clamp because I can't imagine my rabbits sitting there calmly while I try to scratch something illegible in their ear. And I just don't think anyone would be able to read it after I was finished. I've been okay with the end results...the rabbits I've kept as breeding stock still have decent tattoos even two and three years later. I don't show so even if it's faded a little, that's no big deal for my breeders.
As they are tattooed, each rabbit is weighed...and then weighed again every week. This is how I track growth rates of litters and individual animals. I've yet to figure out how to keep track of rabbits and weights without the tattoos. After a few weeks, all REW's tend to look alike to me.
The "number" for each animal is unique - that allows me to mix litters after tattooing. Usually put bucks together and does together until they're old enough they need to be separated.
My clamp allows for a maximum of five characters.
-> First character is for the year. Right now, 2015 is the letter "O". Next year I'd need to use the "O" is around 25 years from now. I'm pretty sure most of the rabbits born this year will be hoppin' around Heaven by then. (I expect I'll be gone by then, too.)
-> Next three characters is for the litter number. 1 through 999. Since I usually have fewer than 99 litters in a year, I only use two digits - but I can go to three if necessary. I track litters on a spreadsheet - so the year and litter number will give me all the info on that specific litter: dam, sire, dates, etc.
-> Last character is for the rabbit itself. A through Z - which will allow for up to 26 kits in a litter.
When I tattoo, setting up the clamp is easy. As I move through the litter, all I have to change is the letter for each rabbit. When I change to the next litter, I just have to change the number - usually just the one digit, increasing by one. I'm usually weaning / tattooing three or four litters at a time. As I tattoo each rabbit, I sex it and add any other notes for that rabbit.
I keep track of who each rabbit is sold to. When that customer comes back and wants another rabbit, it makes it easy for me to get them an animal either from the same line or from a different line. As they give me feedback on how a rabbit is doing, I can make note of that and then see how it relates to the rest of the litter.
Over time, as the rabbits are in the grow pens, they actually get used to having me reach in and look at their ear number. I have a printout of my litter spreadsheet and a copy of the week weights on a clipboard. I kinda hate having to print updated copies so often but it's just too damp/dirty/dusty/rabbit hair/etc. in the bunny barn for me to keep a computer out there. And I don't do smart phones or tablets. (My family would argue that if the computer were out there, I'd never come in the house!)
Okay, enough already. Hopefully you found my lengthy answer of some help.