I found the link to a commercial product by Evrogen to normalise cDNA samples for gene discovery projects here:
The most up-to-date reference seems to be this Curr Protoc Mol Biol. paper by Bogdanova et al.: http://www.ncbi.nlm.nih.gov/pubmed/20373503
They claim their method is compatible with nextgen sequencing platforms:
cDNA normalization using duplex-specific nuclease (DSN) is a highly efficient approach that can be applied for normalization of full-length-enriched cDNA (Zhulidov et al., 2004; Zhulidov et al., 2005). The resulting cDNA contains equalized abundance of different transcripts and can be used for construction of cDNA libraries and for direct sequencing, including high-throughput sequencing on the next generation sequencing platforms (Roche/454, ABI/SOLiD or Illumina/Solexa).
Has anybody successfully used it for next-gen gene discovery projects?