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They are stored in the config files, not embedded in the code.
OracleServiceXE has embedded the port 8080 and 1521
ClrAgent is used for executing PL/SQL wrapper routines written in Microsoft Dot.Net Framework supported languages. If not using that, you can turn it off.
MTSRecoveryService is used for the support of transactions under the Microsoft Transaction Server. If you are not using that, you can turn it off.
The Listener does the same as the OracleListener has done for many versions - listen for Oracle Service connection requests. If it detects a request for a service that it monitors, it attempts to connect the requestor to the service and then steps out of the way.
The definition of Oracle Service has expanded dramatically over the years. For a while it was simply the database. Now the service can include external jobs and EPG requests.
DBMS_EPG is the 10gR2 replacement for the Apache HTTP and provides HTTP, FTP and WebDAV service. It resides in the database. The listener will monitor the network for these kinds of requests on specific ports (eg: 8080) and pass them to EPG.
OracleMTSRecoveryService dewalswith integrationto the Microsoft Transaction Service - a wonderful way of handling distributed transactions under COM+ control (assuming you don't want to use the MUCH easier built-in distributed transaction capability together with heterogeneousservices). Discussed in depth in the "Oracle® Services for Microsoft Transaction Server Developer's Guide"
OracleXEClrAgent provides the host for the Microsoft Common Language Runtime - documented in the "Oracle Data Provider for .NET Developer's Guide" and "Oracle Database Extensions for .NET Developer's Guide"