New tools for analyzing NGS are coming out occasionally. Usually we tend to stick to the same tools just because they work. Well, you may find new tools faster or more accurate for your purposes. Here is a list of tools (and links) which could be used for different purposes (not only RNA-Seq). I could recommend FastQC, FastX, and trimmomatic for cleaning any raw data, and sabre is a nice tool to clean GBS.
FLASH works well for merging reads (there are more tools though) and this seems to be an interesting pre-processing approach. As for sequence aligners, except for bowtie and bwa you may find subread to be fast due to it’s different approach and additional complementary tools for splice alignments, feature counting and SNP calling. Another interesting aligner is stampy which enable to align reads to a diverged reference genome but need some pre- and post- processing to get fast results, otherwise it takes forever.

Of course, there are also some more ‘traditional’ tools for aligning bigger sequences such as MUMer (nucmer, promer) and AMOS. Although these tools are powerful they need some extra pre/post processing which is not always appreciated.