"Lots of keyboard/keystroke mapping differences. Home/End do what they're suppose to instead of what everyother computer platform I've ever used does. Page up / Page down, seriously WTF! Why would anyone ever want them to work that way. Various other oddities like ctrl arrow"

You can customize this if you like. See: http://news.ycombinator.com/item?id=448218

"Half the typical ctrl bindings are Apple key which is in the alt-key position."

You get used to it eventually. I've come to like this more than what having only the control key for most mappings because it allows for more consistent shortcuts (e.g.:, ⌘ is normally used for App/OS shortcuts, while Ctrl is used for Emacs/text-editing shortcuts in all apps)

"No consistent focus follows mouse. No raise on hover"

You can use this command to enable it for Terminal:

  defaults write com.apple.Terminal FocusFollowsMouse -string YES

For other apps, I found this with a quick Google search http://atomicbird.com/mondomouse (haven't tried it myself so I can't say how good it is).

"Can't for the life of me figure out how to get an icon that will open term and ssh into a particular box."

Try this:

  vim logmein
  i#!/bin/bash
  ssh my-box
  <esc>ZZ
  chmod a+x logmein

Speaking of that, here's a nice app for automatically inputting passphrases for ssh: http://www.sshkeychain.org/