There's a template jam-packed with psionic powers that accumulate with HD, called phrenic.

One situation that would be easy to houserule is advanced-animal-HD lycanthropy. If you give most animals extra HD, they increase in size, which alters their stats, so a lycanthrope based on the advanced HD turns into a Bigger Nastier wolf/bear/etc. If your character starts with a standard "base" animal for her lycanthropy, I imagine most DMs would allow adding animal RHD instead of class levels in order to get the advanced version. That costs hit dice, of course, but no more LA.

I agree that it'd be awfully nice to see more LA races and templates that are designed to retain value as you progress.