RDP is a good tool for a quick first look at 16S rRNA datasets, but a suite such as QIIME or mothur will give you much more tools to analyze your data. RDP will classify your samples, but mothur and QIIME will also do e.g. alpha and beta diversity analyses; so they offer a much broader look at differences within your samples. They are especially developed for larger (e.g. 454 or Illumina) datasets. They are a bit challenging to learn, but both offer good online pipeline suggestions and help forums.

Thanks, Ive started to use QIIME. The Genboree online toolkit looks promising, when it is completly up and running.