In general, minconf refers to the minimum number of confirmations, and acts as a filter on results of commands.
IncludeEmpty refers to including the results for addresses which have never received anything. In effect, just listing the address with empty balance and no transactions.
IncludeWatchOnly refers to including the results for addresses where only the public key is known, but not the private key. These addresses are for monitoring what outputs arrive at an address.
Regarding all three parameters, they are used by two Bitcoin API commands.
listreceivedbyaccount ( minconf includeempty includeWatchonly)
listreceivedbyaddress ( minconf includeempty includeWatchonly)
You can find out more here:
In a nutshell, listreceivedbyaccount retrieves the balance for an account of the wallet, however accounts are deprecated in Bitcoin-Core so you can ignore this API call. You should use getbalance instead.
Listreceivedbyaddress will return the transactions received by each address in the node's wallet, and you can filter the results by number of confirmations etc.