Usually I keep the default appearance, unless something about it bugs me or if I have two toons of the same class (that way in my head they're different people, cause I'm silly).
Doc - I had to lose his soul patch thing, ugh, just ugh. So I went with Doc 3. http://www.torhead.com/item/eHu2LoQ/doc-customization-3
Iresso - Something about the default Iresso's face just didn't work. Went with Iresso 6. http://www.torhead.com/item/6zOIkUD/...ustomization-6
Zenith - Not a fan of that weird melon green. I have two JCs so my sage's Zenith is Zenith 2 http://www.torhead.com/item/2NDCiSX/...ustomization-2
and my shadow's Zenith will be Zenith 8 http://www.torhead.com/item/9Tsevsh/...ustomization-8
Qyzen - Had two different ones, so picked out some random colors. No particular reason. Sage has Qyzen 1 http://www.torhead.com/item/5oc4yxQ/...ustomization-1
and shadow has Qyzen 3 http://www.torhead.com/item/aE3EvZ3/...ustomization-3