Best way of adding SNMP support to your own application on Debian

net-snmp supports both the smux and agentx agent extension protocols, allowing sub-agents to live in different processes. They also have a tutorial on writing AgentX subagents in C.

An often overlooked solution is Agent++ API, which to me looks pretty nice and is under the Apache license. As far as I understand, you can modify that agent to answer to your own MIBs.

That said, doing a subagent isn't such a bad choice. You start the standard unpatched snmpd (from net-snmp). Then you connect to it with your subagent, which only adds those OIDs you want it to add. The net-snmp kit for coding AgentX (as the protocol is called) sub-agents is not dead simple to use, but not very hard either. There is also a Perl module for sub-agent development: https://metacpan.org/pod/NetSNMP::agent

The traditional way to do this in linux is to use the net-snmp package. Make sure you write the MIB first. Everything is based on the MIB and changes to the MIB usually results in lots of changes in the code. Coding for net-snmp is not difficult and there is lots of documentation to get you started, eg: http://www.net-snmp.org/wiki/index.php/Tutorials#Coding_Tutorials