Set “Always on Top” for a window

There is no "native" way to do this. Your existing solution, Afloat, is the only one I've ever heard of (and works quite well).

In Terminal you can change the default window size from Preferences > Settings > Window:

You can also use window groups to set a default position and size for the window opened when you launch Terminal (but not for new windows opened later).

I use Sequential and Skim as alternatives to Preview and iTerm 2 as an alternative to Terminal. All of them have an option to open windows in full screen by default, and all of them have their own (pre-Lion and actually usable) implementations for full screen windows.

The sizes of Finder windows are saved in .DS_Store files and there are no default window size settings in com.apple.Finder.plist or anything. I use a script like this to reset the properties of windows:

tell application "Finder"
    if number of Finder windows is 0 then return
    tell Finder window 1
        set toolbar visible to false
        set sidebar width to 0
        set statusbar visible to false
        set current view to column view
        set bounds to {960, 44, 1920, 1076}
        tell its column view options
            set shows icon to false
        end tell
    end tell
end tell