Tophat is a tool to align RNA-seq reads, Cufflinks assembles transcripts, and estimates their abundances
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Istvan Albert
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RNA-Seq: a revolutionary tool for transcriptomics. Zhong Wang, Mark Gerstein & Michael Snyder, Nature Reviews Genetics 10, 57-63 (January 2009)
Next-generation transcriptome assembly. Jeffrey A. Martin & Zhong Wang Nature Reviews Genetics 12, 671-682 (October 2011)
RNA sequencing: advances, challenges and opportunities Fatih Ozsolak & Patrice M. Milos, Nature Reviews Genetics 12, 87-98 (February 2011)
RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing Brian T. Wilhelma and Josette-Renée Landryb, Methods Volume 48, Issue 3, July 2009, Pages 249–257
I am going to add the checkmark to any post that is merged into the toplevel one
Models for transcript quantification from RNA-Seq, Lior Pachter, preprint arXiv 2012
Computation for ChIP-seq and RNA-seq studies. Pepke, Shirley; Wold, Barbara; Mortazavi, Ali, Nature methods. 2009 6(11 Suppl):S22-32
Molecular Ecology
Nagarjun Vijay Jelmer W. Poelstra Axel Künstner Jochen B. W. Wolf
RNA-Seq Assembly – Are We There Yet?
Simon Schliesky,1 Udo Gowik,2 Andreas P. M. Weber,1 and Andrea Bräutigam1,*
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Here is a review/educational paper "Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud" that accompanies an extensive hands-on tutorial at rnaseq.wiki. It covers many aspects of RNA-seq and includes primers on related fundamentals that you will need including Unix, R, Genome Browsers, using cloud computing, etc.
Update 2016;
http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8