Sears is one of the few stores that seems to have a decent selection at cheap prices. I picked up a ton of $0.97 GBA games there over the last two months (stuff like Klonoa 2, Megaman Battle Network 5, licensed fare, etc) as well as Pokemon Emerald ($4.97), Final Fantasy V ($9.97) and Final Fantasy VI ($4.97 - $9.97).
KMart also has a decent selection of GBA games. For example some games I got there recently include Legend of Zelda: A Link to the Past ($4.99), Super Robot Taisen Original Generation ($5.99), and Yu-Gi-Oh! World Championship 2004 ($9.00). They also had Mega Man Zero 4 for $14.99, and a few other titles around that price as well.
I would suggest checking the KMart Clearance thread and the Sears clearance thread in the main forum for a more complete picture of GBA titles people have been picking up.