For the record, I'd like to state that the newer S25FL2 series works with Altera FPGAs. I was able to configure a Cyclone IV E with the S25FL216 (2M x 8) device, and it would likely work with other FPGAs.
I know about the use of Spansion's S25FL series SPI flash to configure Altera devices. [1] However, S25FL is going to be obsoleted (if not already) and replaced with the S25FL2 series. I couldn't find anything from Spansion (or elsewhere online) that explicitly confirmed that S25FL2 will work as well, even though Spansion says it can replace the older models "in many applications." [2] I wasn't 100% sure if the S25FL2 series would work as an Altera configuration memory until I tried it out successfully.
[1] Search for "Configuring_Altera_FPGAs_via_SPI_Flash_AN.pdf"
[2] Search for "Migrate_FL-K_to_FL2-K_AN.pdf"
