First off, I would mention that as good as eartags are for ID, they aren't fool or tamper proof. I have yet to see a tag that couldn't be removed, even the little metal ones can be. For permanant ID a brand is best, it can't be removed.
Now, having said that, for in herd ID, tags IMO can't be beat. We use Y-tex tags, and rarely have a problem with lost tags. If we do have a lost one it is almost always due to twine.
We simply tag them in order 1,2,3,4.... Usually in the order they come down the chute. We also reuse the tags, and numbers, so if we cull someone we will use her number in a heifer or something that we bought.
For extra ID, I have been using metal tags with an individual # for each animal. That way if we have 2 look alike cows without tags I can crossreference them. I have started to tattoo all our heifers with a year letter and number so that will replace the metal tags.
For our calves, we color code them according to sex, and whether they are lease calves or our own calves. The calves recieve the same number at birth that their mother has for ease at sorting time. When we wean we remove all the herd ID tags from anything going to the sale barn. Any heifer that we keep will just get a random (leftover) number. All our sale animals are also tagged with RFID tags.