So if you see something along the lines of this

root@kali:~# hydra -s 443 -S -l admin -p adminpass  https-post-form  "/php/a:user=^USER^&pass=^PASS^:DENIED"
[VERBOSE] Could not create an SSL session: error:14077410:SSL routines:SSL23_GET_SERVER_HELLO:sslv3 alert handshake failure
1 of 1 target completed, 0 valid passwords found
Hydra ( finished at 2015-03-24 21:52:57
Then grab the latest version from git and enjoy breaking in once more
root@kali:~/git# git clone
root@kali:~/git# cd thc-hydra/
root@kali:~/git/thc-hydra# ./configure 

root@kali:~/git/thc-hydra# ./hydra -s 443 -S -l admin -p adminpass  https-post-form  "/php/a:user=^USER^&pass=^PASS^:DENIED"
[443][http-post-form] host:   login: admin   password: adminpass
1 of 1 target successfully completed, 1 valid password found
Hydra ( finished at 2015-03-24 21:57:29

So why is this? It's because, by default, Hydra used just an SSLv3 hello no matter what as that is what everyone supported, but since SSLv3 has been depreciated and has found itself in the sights of PCI you will find more and more sites turning SSLv3 off. You may encounter this in other tools as well, most of the time they just need rebuilding or an extra flag adding. As a side bug once you try and fail to use sslv3 on one of these servers Hydra will skitz out and start flooding the target with requests, OOPS!