Lews Therin and his Companions put the seal on the Bore and supposedly locked away the Dark One and all of the 13 Forsaken. But in the prologue of The Eye of The World which happened after this, Ishamael meets Lews Therin, also there are multiple indications in the first book that Ishamael was never imprisoned. If that's the case, why did he wait for three thousand years? He could have done a lot of bad things, maybe even become the ruler of the whole world? What was he doing all that time?
He was doing "Bad Stuff"
The wiki lists two possibilities on whether he was trapped or not. He was either A. half sealed and able to be spun out of the prison, or B. never trapped.
One of the important things to remember about Ishamael was that he was insane, so the things he supposedly did may not make sense to a non crazy, non evil person. The wiki also only knows of two of his adventures, but they are incredibly important to the Wheel of Time history.
According to the wiki, he, under the name of Ba'alzamon, raised a trolloc army and attacked, and destroyed Manetheren.
His most devastating action during the Wars was when he led the Shadows forces in directly assaulting Manetheren. The attack destroyed Manetheren and allowed the Trolloc armies to ravage nearly all of the Westlands.
He then disappeared after 40 years, and the trolloc army is destroyed.
He then becomes the chief advisor to Arthur Hawkwing under the name of Jadwin Moerad. It was he who encouraged Arthur to lay siege to Tar Valon.
He set about wrecking that which Hawkwing had built, advising him to dismiss all Aes Sedai from his service, lay siege to Tar Valon, send his armies across the Aryth Ocean, and refuse Healing on his deathbed.
After Hawkwing's death he basically sows chaos into the main contenders to the thrown by killing many of them. Then, after 40 years, he vanishes.
Personally I agree with the theory of Aran son of Malan son of Senar, who stated that Ishamael could be spun back out into the pattern for as long as 40 years to do evil and, in response to your question, he did.
*I got this information from the WOT Wikia article on Ishamael. If anyone wants to find the original source I believe (I have sadly not read it) that the information comes from The World of Robert Jordan's The Wheel of Time.