For Illumina RNA-seq data, I've used simLibrary and simNGS (http://www.ebi.ac.uk/goldman-srv/simNGS/) in the past to simulate transcriptome reads. The following commands will simulate a FRTseq (--bias 1) library construction of average insert size 300 (--readlen 300) of a transcript CDS sequence, producing the input to be sequenced. The gel_cut option makes sure you only sequence above 200bp and below 1000bp. In the transcript CDS sequence you can add UTRs or introns if you want:
After that, I rename the sequences for tracking (scripts available here http://github.com/avilella/hashbrown) and run them through simNGS for 125 cycles, paired-end, producing the output fastq files.
The runfiles contain information about the intensity values given by a real machine for a real run. There are different example runfiles available in simNGS, both from real Illumina GA2 machines and Illumina HiSeq2000 machines. The runfiles have comments about when/where was the sequencing done, how well did it go, etc. If you want to simulate data as close as existing sequencing runs that you've already done in your facility, you can build your own runfiles using AYB against example .cif files from your own sequencer.
Hope it helps.