Which legendaries are worth the investment for stardust?

Assuming you've already put aside enough dust to max Mewtwo (because he's the best duh), Raikou has the biggest niche as a water counter, and the biggest edge over its non-legendary competition (jolteon). I'd go with Mewtwo and Raikou.

I would add Moltres aswell.
Top 5 attacker, if you still have enough to invest on a fire type pokemon, Moltres is best choice over Ho-oh and Entei.
Ho-oh has the 2nd highest CP in game, but its attacks are awful, and his best set doesn't give him STAB, so Entei is still better than Ho-oh.

If you have multiple perfect legendary max them all , duh.

If you have any legendary, max that!

None.