The best labeling system (in terms of long-term archival safety) is no label at all. Use the serial numbers pre-printed on the discs' hubs to cross-reference to an external database. Obviously, this isn't very convenient.
The second best label is a hand-written label, using a CD-labeling pen, on the clear hub area.
The third best label is a hand-written label, using a CD-labeling pen, on the labeling area of the disc. Generally this is anywhere on the top of the disc, but sometimes discs have specific areas set aside for labeling.
If you don't like the idea of hand-written labels and are willing to spend the extra money for the printing systems and compatible discs, you might want to look into the ink-jet or thermal printing systems. I don't know, however, what effects these types of systems have in terms of long-term archiving.
Probably the worst choice you could make is to use any of the adhesive labeling systems. These labels can unbalance the disc, peel up around the edges, delaminate the top reflective and data and layers of the disc, corrode the disc due to chemicals in the adhesives, etc.
In any event, make sure to use high-quality discs, store them in cool, dry, dark conditions, and test them on a regular basis so that you can detect any problems before they become so serious that the data can not be recovered and re-written to new discs.
Depending on how valuable your data are, you also might want to make two copies of each disc, using different brands and dye types (e.g. one on TY-cyanine and one on Ritek-phthalocyanine or Mitsubishi Chemicals-SuperAZO) and store them in two different buildings. Recording on two different brands gives you extra protection against bad batches of discs or dye related failures. Storing the copies in different locations gives you extra protection against physical disasters such as fires and floods.
Here are some additional resources you might wish to explore:
http://www.itl.nist.gov/div895/careford ... /index.htm