I used Pageant to add keys to it from a C# code behind. I found that I can use the command line to add keys to Pageant described here:
http://the.earth.li/~sgtatham/putty/latest/htmldoc/Chapter9.html#pageant-cmdline
It works fine, but I start thinking how can I remove a key from Pageant using the command line client? Is there any way to remove them somehow? After a while I have a lot of loaded keys from different users and I think that is the reason why the authentication method doesn't work well.