There was a hot discussion that RPKM should not be used in the RNA-seq analysis:
blahah404 Woohoo - death to FPKM and RPKM
However @BioMickWatson has a different opinion, he thinks FPKM makes sense.
Why FPKM makes sense
what is RPKM or FPKM? see blog posts below:
update on 07/23/2015, see a youtube video for great explanation of the three.
What is the FPKM? A review of RNA-Seq expression units
Counts vs. FPKMs in RNA-seq
Paper: RPKM measure is inconsistent among samples
FPKM/RPKM normalization caveat and upper quartile normalization
Finally a post from Lior Pachter
Estimating number of transcripts from RNA-Seq measurements (and why I believe in paywall)
I personally use raw counts and let DESeq2 to deal with normalization.
update on 07/08/2016.
Salmon and Kallisto outputs TPM, but if you want to convert counts to TPM, read this biostar post, and my post comparing salmon, kallisto and HTseq.