I know of two excellent articles describing the impact of software on EMC. The main impacts are related to making the design robust and resiliant to electromagnetic disturbances to make sure the product can pass susceptibility tests. Both articles also mention how software can affect the emissions profile of a product as well. The latter article contains some practical steps that can be taken in software to minimize emissions [2]. To summarize these techniques:
[1] O'Hara, Martin. September 2007. "The EMC Impact of Embedded Software." Conformity.
[2] Brotz, Joseph. May 28, 2008. "Software Techniques for Comprehensive EMC Testing of Embedded Systems." Emedded.com.