It's still the only SSH client I know that can change most of its settings during an existing session, especially in a cross-platform way (it is available for Linux). Good software indeed.
Are you talking about tunnels and port forwards?
OpenSSH can do that - you type in an escape sequence and you can work your magic on the fly.
Some of these could be changed in various more disjointed ways in Linux or Windows, but it's nicely unified and cross-platform in PuTTY.
I'll admit I rarely leverage this flexibility, but it's cool enough that it seemed worth noting in this sub-thread about singing PuTTY's well-deserved praises.