As mentioned above by some people I have always attributed this to CD Rot. I don't think it as much depends how you store them or where they are as much as how they were manufactured. Most of the times they have narrowed this problem down with commercial discs - it has always been a flaw in production. I have also heard the only way to prevent it from happening (after a disc has already been poorly manufactured) is to put the discs in a fridge or freezer within a ziplock baggie. This will help it not to oxidize as quickly or not at all. I have been dealing with this since Laserdisc - so it is not shocking to me. They have still not even perfected Blu-Ray and HD DVD from this same optical disc plague. h:
For long-term, archival backups, I highly recommend HDD storage, mirrored on to two drives, stored in two separate locations. Expensive, yes, but that will extremely reduce the likelihood of lost data. Rip optical media to ISOs, and re-burn from the source file when the CD-R/DVD-R takes a dump.
Are flash drives unreliable? I was thinking of getting like, 2 4GB ones or something. I don't have a ton to back up that is irreplaceable.
Flash Memory will fail on you too. When I bought my PowerPAK with the 128mb CF card, I noticed all sorts of problems shortly after starting to use it. File would randomly be non-accessible or bytes would change to different values. No form of data storage is 100% reliable. Multipule backups certainly would help so if you have flash drive backups for you important data it doesn't hurt.
Though purists may look down on them, this is why I like ROMs, ISO's, box scans etc up on the web shared by collectors and downloaded by many, preserving the files by virtue of never rotting in the basements of a few collectors. If I can get my hands on more abandonware FM Towns games, I will immediately put them in ISO format and share them with all who are interested.
Another method is to convert backup data to binary and hand write all the 1's and 0's to a note pad. :icon_bigg
Don't ever store valuable data in a sleeve. Keep it in a plastic case in a dry place at room temperature.