How to highlight just the name (not the extension) for renaming?

Use something else than Nautilus' List View mode. It works fine in the Compact View and Icon View modes. Apparently it's a regression: https://bugzilla.gnome.org/show_bug.cgi?id=627110

Update:
This is now fixed in the development version of Ubuntu 11.10 (Nautilus 3.0.1.1).

When I right click a file and select Rename, or press F2, the extension isn't highlighted.

To answer your question: you don't have to do anything.

You should try pressing F2 twice and extension will highlight.

to get only name without extension:

${var%.ext}

where ".ext" is extension

following a test script. to effect changes alter the commented line

for name in `find ./path -iname "*pattern*.ext" `; do
    new_name=${name%.ext}newextension
    if [ "$new_name" != "$name" ]; then
        echo “$name => $new_name”
        # mv “$name” “$new_name”
    fi
done