Well, you've missed a lot although the comic book related characters didn't start showing up until probably late season 3 with Perry White in the episode "Perry."
But, earlier in Season 2 there was the visit Clark made to Dr. Virgil Swann (played by Christopher Reeve) who explained to him where Clark had come from.
Dr. Swann made another visit in Season 3 and explained more to Clark in the episode, "Lineage."
In season 4 Lois showed up in the season preem, "Crusade."
Also in Season 4, Bart Allen (the Flash) showed up in "Run" and Mzxyptlk showed up in "Jinx." (Although not everyone was a fan of that particular take on the character.)
At the end of Season 4, Clark got all the stones together that formed the crystal that would build the fortress of Solitude in "Commencement."
Brainiac, aka Milton Fine, showed up in the 5th season preem, "Arrival." He played a strong role in several episodes in the first half of that season, leading up to the reveal of his real plan in "Solitude." He would come back to try again, tricking Lex into doing his work for him, by the end of the 5th season to free Zod from the Phantom Zone in "Vessel."
Aquaman showed up in the fifth season ep, Aqua and Cyborg (Victor Stone from the Teen Titans) showed up later that season in Cyborg. (One of the best episodes of that season, actually.)
Clark was stuck in the Phantom Zone in the 6th season opener, "Zod," while Zod was turning Earth into the new Krypton.
Oliver Queen showed up early in Season 6 and stayed around off and on up until "Justice." Jimmy Olsen also showed up in Season 6, saving Chloe from the chaos in "Zod."
We didn't really see anything else related to any new DC comic related characters until the season ender that aired last thursday, "Phantom," which introduced Smallville's take on Bizarro.
I have no idea why I took the time to explain this, maybe I was bored, but I hope it's helpful. The show has changed a lot since the 2nd season... you should rent the DVD's.
Brainiac was awesome last year but this year, overall, has been the best ever in my opinion.