compmerge is a program that tries to solve the same problem as cuffmerge.It is not limited to cufflinks models and transcripts, but can work with any .gtf file.It merges the spliced transcripts that have a compatible intron structure and merges the monoexonic transcripts based on simple stranded overlap.The output is a .gtf file of merged transcripts.
After getting the compmerge executable, type:
without any argument to get the help.
This will give you all the possible options of compmerge.
Do not hesitate to contact sarahqd at gmail dot com for more information.