Could we compile a growing list of all the different sequencing applications? This could be accompanied by a short description for tyros.
RNA-Seq involves sequencing of transcriptomes consisting of different species of RNA (e.g. mRNA) as cDNA. It provides a good picture of transcript abundance as well as transcript-processing events. Wikipedia page
ChIP-Seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. Wikipedia page
ChIP-Exo is a modification of the ChIP-seq protocol, improving the resolution of binding sites from hundreds of base pairs to less than one base pair. It employs the use of exonucleases to degrade strands of the protein-bound DNA in the 5'-3' direction to within a small number of nucleotides of the protein binding site. Wikipedia page
miRNA-Seq Wikipedia page
DNA-Seq SEQWiki page
Methyl-Seq Wikipedia page
RAD-Seq University of Edinburgh page
GRO-Seq is the name for Global Run-On sequencing. See more details here: ngsbioinformatics.com page
NET-Seq is short for Native Elongating Transcript sequencing. It involves immunoprecipitation of RNA polymerase followed by sequencing bound RNA fragments Nature paper
FAIRE-Seq is the name for Formaldehyde-Assisted Isolation of Regulatory Elements following by sequencing. Check out a description here: Wikipedia page
Ribo-Seq consists of freezing ribosomes to capture bound mRNA in the process of translation. After the ribosomes are primed open the mRNA fragments are sequenced. Science page
Update: Here's a much better list: Lior Pachter's list of *Seq
I would suggest that you edit the main post and add the new answers as they appear
Splendid idea. I'll keep an eye on this post.