Seems to be a hot topic right now. This is from the Globe and Mail but I’ve copied the text here as I don’t know how long they archive these things.

Appears storing CDs on the spool may not be a great idea as they recommend storing them vertical and being very careful of the tops (yes, you read that correctly, the top!) The recorded surface is closer to the top than to the bottom, so therefore the top is more sensitive to damage. More likely that a minor scratch on the top will expose the recorded layer to the air, which will then cause mold and rust to accumulate.

I’ll have to reconsider my storage of backups. I guess I’ll need a lot of jewel cases now…

Do:

1. Handle discs by the outer edge or the centre hole. Your fingerprints may be acidic enough to damage the disc.
2. Use a felt-tip permanent marker to mark the label side of a CD. The marker should be water-based or alcohol-based. In general, these will be labeled "nontoxic." Stronger solvents may eat through the thin protective layer to the data.
3. Keep discs clean. Wipe with cotton fabric in a straight line from the centre of the disc toward the outer edge. If you wipe in a circle, any scratches may follow the tracks of the CD, rendering them unreadable. Use CD/DVD-cleaning detergent, isopropyl alcohol, or methanol to remove stubborn dirt.
4. Return discs to their plastic cases immediately after use.
5. Store discs upright (book style) in their cases.
6. Store discs in a cool, dry, dark place with clean air.
7. Open a recordable disc package only when you are ready to record.
8. Check the disc surface before recording.

Do not:

1. Touch the surface of the disc.
2. Bend the disc. This may cause the layers to separate.
3. Use adhesive labels, since they can warp the disc or unbalance it.
4. Expose discs to extreme heat or high humidity. Don’t leave them in sun-warmed cars, for instance.
5. Expose discs to extremely rapid temperature or humidity changes.
6. Expose recordable discs to prolonged sunlight or other sources of ultraviolet light.

For CDs especially do not:

1. Scratch the label side of the disc. It’s more sensitive than the transparent side.
2. Use a pen, pencil, or fine-tip marker to write on the disc.
3. Try to peel off or reposition a label. Again, you risk unbalancing the disc.