After Athens' victory in the Persian War (around 448 BC), it was leader among the Greek poleis in the realms of politics, economics, art, and literature. They were seemingly untouchable, except by perhaps the Spartans. This period of power and prosperity is known widely as the Classical Period of ancient history, and the benchmark of the period of the 5th and 4th centuries BC, the culture against which all other cultures have been measured, was Athens.
During the Classical period, Athens enjoyed the support of other poleis, and was able to fend off other Persian attacks. And after its defeat at the hands of Sparta in the Peloponnesian War (around 404 BC), Athens, though never able to fully regain its wealth and importance, did enjoy brief periods of prosperity until the arrival of Philip of Macedon, and the onset of the Hellenistic period of ancient history.
Through all of this, the Athenian Agora remained an important aspect of Athenian society and culture. While Athens had sworn an oath to not rebuild the cherished temples that Persia had destroyed (the Oath of Plataia), they did rebuild some of the civic buildings, while constructing new buildings that were indicative of the economical and political prominence of Athens from that time.
It was also during this time that the legendary Athenian general and leader Pericles began his significant building programs on the Athenian Acropolis. Therefore, building in the agora was intermittent. However, many important buildings were added and rebuilt in the Agora. And while it is easy for the beauty and grandeur of the Acropolis to overshadow the Agora, one must not discount its importance to Athenian history, as well as its artistic and architectural significance. Though not equal to the building program on the Acropolis, the Agora certainly worked to bring balance to the city.
During the hard-fought Peloponnesian War against rival polis Sparta, Athens, as a show of its strength and determination, continued its building in the Agora. More modest materials such as limestone, mud brick, and earth floors were used in place of the Pentellic marble that Athens was famous for, but progress continued nonetheless.
After the loss to Sparta in 404 BC, Athens turned its attention to recouping what wealth it could, rather that building construction. Soon after, Athens lost its prominence in the ancient world, and the Agora saw little development from there. But its importance as a center of commerce, politics, philosophy, and law cannot be denied. We see it today in the Palazzos or Italy.