Essentially, there is little difference in quality between CD-R's and replicated CDs. CD-R's are a cost-effective option for short-runs of 1-499. They're also the best option if you have a really tight deadline since duplication is a quicker process, but you will pay alot more than you would for replicated discs if you're ordering over 500 units!
CDs are manufactured so that your data is embedded into the disc but they do take longer to produce due to glass mastering etc. If you were going to get more than 500 CDs pressed I'd definitely go with replicated CDs.