The general consensus seems to be to NOT remove duplicates from RNA-seq. Read the biostar discussions:
and this seqanswers thread and the other threads it links to.
I really depends. I have seen alignments with so many same reads at a certain position (5 and 3 prime exactly matching), that it were for sure PCR duplicates (on other positions in the alignment there was no such coverage). However, you might loose information about strongly expressed genes this way. I would check for un/equal coverage for every gene/contig.
If you have paired-end reads, I definitely think you should remove duplicates (alignments that start at the same locations at both read 1 and read 2). These are very unlikely to occur by chance because of the variation in fragment size.
If you have a small amount of RNA going into the experiment, you will have run a lot of PCR cycles before sequencing and the representation of some fragments will have become very biased. Duplicate removal is a way to mitigate this effect although it will not solve it.
It continues to baffle me why people keep saying that you have to keep duplicates because you will lose information - but apparently it's perfectly fine to get grossly distorted read counts because of amplification artifacts! There is no way to avoid bias completely.
The EXPRESS pipeline (berkeley) does this for you. It calculates a coverage distribution and then removes the "spikes" from that distribtion. Because duplicates are expected in RNA Seq, removing them "blindly" is a bad idea. You should be smoothing, not removing.