You can arrange for Pageant to start another program once it has initialised itself and loaded any keys specified on its command line. This program (perhaps a PuTTY, or a WinCVS making use of Plink, or whatever) will then be able to use the keys Pageant has loaded.
You do this by specifying the -c
option followed by the command, like this:
C:\PuTTY\pageant.exe d:\main.ppk -c C:\PuTTY\putty.exe