Ideally I would be close enough/have enough reach so that I wouldn't have to do any cropping, but that is rarely the case unfortunately. Usually I just crop an image as much as I feel is needed and then let that limit what I will use the image for.
I find it useful to keep an uncropped or less cropped .PSD file just in case. I don't know of a way to crop an image as a non-destructive edit, and if you do end up needing particular dimensions or need to include a little more background to increase the pixel count a bit for printing or something you would need to start over with the RAW file.
I have examples of really cropped pictures and others I haven't really cropped at all, but I'm not sure if it would help anyone out to see them. I took a few pics today of a hawk that we keep seeing when we take the dogs for a run that we would like to try to identify. I have them cropped down to 100% and it doesn't look that great, but they are pretty useful for identification purposes. (we think we may have a rough-legged hawk but the identification is inconclusive ...)
coastalconn, a zoom lens will most likely require a different AF Fine Tune value at different focal lengths (and different apertures I believe) so it is best to calibrate it to how you shoot most regularly. For this reason, AF Fine Tune works best for primes. I think it's a case of the more you know your lens, the better. I am impressed with the sharpness that you are getting out of your Tamron @ 500mm by the way. I am hoping to upgrade my telephoto in the next year and you are making a case for those long zoom lenses ...