I ran into the too-many keys problem a while back. I currently have 15, but hit the limit on several servers when their keys were pushed beyond 6th in the list. The workaround is to use IdentityFile to specify which key you want to use for the server. In ~/.ssh/config:
Host example.com
IdentityFile ~/.ssh/key_for_example.com
Best,
Ben
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Link to this comment: http://www.securityfocus.com/comments/infocus/1812/1222#1222