Completing each puzzle reveals a message written on the ground in Unown. The messages are different in Crystal and HGSS.
Completing the Kabuto puzzle reveals the following message:
Our words shall remain here for the ages (Crystal)
Our clan engraved words in this place (HGSS)
Completing the Aerodactyl puzzle reveals the following message:
Thus we shall erect a Pokémon statue outside (Crystal)
Our clan created a Pokémon statue outside (HGSS)
Completing the Ho-Oh puzzle reveals the following message:
We humans must learn to walk in harmony with them. We depart for their sake (Crystal)
We humans need to walk with them. We leave here for the sake of them (HGSS)
Completing the Omanyte puzzle reveals the following message:
They possess great insight and refuse the outside world (Crystal)
They possess the power to sense with their mind and reject outside (HGSS)
Bulbapedia Ruins of Alph page