GNS3 comes by default with PuTTY as the main console application, however you can configure it to use SecureCRT.
Got to: Edit -> Preferences -> General -> Console Application
and change Console application command field to:
c:\PROGRA~2\SecureCRT\SecureCRT.exe /T /N %d /telnet 127.0.0.1 %p
To restore PuTTY use:
putty.excodeelnet %h %p -wt “%d” -gns3 5 -skin 4