Bonjour services are installed without explicit user permission and the software is often not necessary for running the programs that bundle it. While there are no documented conflicts with anti-virus software packages or the Microsoft Windows operating system, some corporate firewalls may raise a warning when Bonjour attempts to broadcast the availability of network services.
Some technical forums have reported that the service can break a configured internet connection and also can conflict with system files on certain versions of Windows. Other programs with which it interferes include Juniper Network Connect, a VPN client.
Stability of the software varies with each version. Misbehaviour on larger corporate or ISP networks caused when Bonjour issues excessive or malfunctioning broadcasts is not welcomed by IT managers, especially given the limited technical support Apple provides for this product. Users who manually disable the service will often find it re-enabled by Apple's regular software updates
Like many zeroconfig networking tools, user customization is non-existent. This often causes unnecessary and unwanted network traffic that cannot be stopped unless the service is disabled completely.
Older versions of Bonjour have compromised network security and even the most up-to-date versions are known to cause issues with Zero Configuration tools offered on modern laptop computers.
Uninstalling the software from Windows is usually problematic, due to a poorly implemented and deliberately hidden uninstaller. After uninstalling Bonjour, it commonly leaves processes running in the background. mdnsresponder doesn't show up in one's TCP/IP stack (and causing corruption) using tools such as lspfix.exe until after killing the leftover processess, deleting the process files and then rebooting.
The method by which Bonjour is installed on a computer without notice and the fact that it does not come with a true uninstaller means Apple Computer and the Bonjour service may contravene strict European laws governing that have been used against Microsoft in the past.
http://en.wikipedia.org/wiki/Bonjour_(software)