There are lots of good reasons for making the effort to incorporate third party applications into EMBOSS. Just a few are listed below.
Distribution. It's clearly desirable to reach as many users as possible. EMBOSS has thousands of users and many sites regularly download the latest release, so any software that's incorporated will be widely distributed.
Training Cost. Incorporated software is used in exactly the same way as all other EMBOSS applications. Someone familiar with EMBOSS will be able to use any application that's been ported or wrapped. There's no additional training requirement beyond, of course, learning about the specific methods the application implements. That is a requirement regardless of whether or not an application is in EMBOSS.
Support Cost. Incorporated applications will benefit from a basic level of support provided by EMBOSS through the mailing lists. The level of support depends on the circumstances. An application that's been fully ported with the understanding of it being adopted by EMBOSS would be fully supported. At the very least a user would get a reply to any email query and forwarded to where they could get more help. This is especially valuable in cases where the original author of an application has since moved away from the institute that now maintains it.
Maintenance Cost. There might be savings on the maintenance costs. This again depends on the level of integration and the specific arrangements. At the very least EMBOSS would investigate any bugs and forward appropriate reports to the authors of the original software. There is an additional cost to maintain the port or wrapper as well as the original code, but this is more than offset by the benefits.
Web Services, Workflows and Interfaces. EMBOSS has been incorporated into many graphical interfaces and workflow software such as SRS, Pipeline Pilot, Taverna, wEMBOSS and Jemboss. Further, thanks to on-going developments in SOAPLAB, it is relatively easy to deploy an EMBOSS application as a web service. If your software is incorporated then there's little or no additional cost in setting it up in these contexts.
Database Support. EMBOSS supports all the common formats for input and output of sequences, sequence features and sequence alignments and is moving towards using standard application report formats for output. Many other common data formats are supported. Any software you incorporate will be able to use these formats too. What's more, when EMBOSS is updated to support changes to the formats, or entirely new formats, then your software will automatically benefit from these changes.