Can you be more clear about what "PuTTY Agent" does? The only PuTTY I'm aware of is an open-source Windows SSH client. The Mac Terminal program has an SSH client inside of it, although it can be a little difficult to use. If you want a commercial SSH GUI that's fully featured and has a better UI then I will recommend SecureCRT available from VanDyke software. SecureCRT is also available for Windows and Linux. It's pretty much the same application on all platforms and I find really great to use.
If you make shortcuts, and if there are a lot of them, you still have to organize them somehow. I want some kind of application, like the Microsoft RDP client, where you open the application and it is organized by groups and servers.What's wrong with setting up ssh with a config file that contains shortcuts for all your servers? That's not complicated.