I like to work in a tabbed SSH connection manager. Especially when I have hundred's or thousands of machines to connect to. A connection manager like putty keeps track of machine names and login info. Using a tabbed interface like MTPutty can make your life a whole lot easier with treeview/groups and side by side terminals. And additionally if you can cluster the terminal commands it can be an added bonus.

So far I have not really liked anything in the Linux world as far as a SSH connection manager. Ubuntu does come with putty which seems to work the same as in the Windows world. Best I could find is an application written in Python called Gnome Connection Manager (gcm). In the Ubuntu 15.10 repos the package is called gnome-connection-manager. Be warned of a few things:

1. Seems the code is at least a few years old and the website does not seem to have documentation or any kind of discussion. The code is all python so you can look at fixing and emailing the owner.
2. Be sure to check the paste-right-click in ~/.gcm/gcm.conf. This can be a nasty setting if you did not expect it. I copy and paste a lot between a Windows desktop and a Linux guest and almost accidentally pasted garbage into a critical device.
3. Also check auto-copy-selection if you like putty style behavior where anything selected in your SSH terminal should be in the copy buffer.

I think if the developer put a little bit more love into gnome-connection-manager it would definitely be a keeper and first rate gnome app. I have looked at some other options like hotssh but worth checking out is Remmina. Unfortunately for me Remmina was very buggy.

I recently needed to copy files using scp, while not able to copy directly to the target host.  I had to use an intermediate firewall host.  There is a few ways to get this done and most requires netcat (nc) on the intermediate host for copying.

Keep in mind using -t for just a ssh shell connection will work:

$ ssh -t rrosso@backoffice.domain.com ssh admin@10.24.0.200

If needing scp below is a way to get this done when netcat is not a possibility.

In a new terminal do this (command won't return a prompt and leave the terminal open):

$ ssh rrosso@backoffice.domain.com -L 2000:10.24.0.200:22 -N

In a new terminal ssh as follow:

$ ssh -p 2000 admin@localhost

Scp as follow:

$ scp -P 2000 testfile admin@localhost:/tmp

Sftp also possible:

$ sftp -P 2000 admin@localhost

Update 1:  Above will work fine but you can also consider the following to make things more transparent.

$ vi .ssh/config
Host *
 ServerAliveCountMax 4
 #Note default is 3
 ServerAliveInterval 15
 #Note default is 0
#snip
host work-tunnel
 hostname backoffice.domain.com
 port 22

 # SSH Server
 LocalForward localhost:2000 10.24.0.200:22
 user rrosso

# Aliases as follow
host myhost.domain.com
 hostname localhost
 port 2000
 user admin

Then run the tunnel connect first (use ssh -v while still troubleshooting):

$ ssh work-tunnel

Leave above terminal open to leave tunnel going. And now you can run commands in new terminals with syntax as if no tunnel required.

$ scp testfile myhost.domain.com:/tmp
$ ssh myhost.domain.com

That should do it for a ssh shells.

Example for other ports:

Note you can do a lot of other ports also in similar fashion.  Here is an example you could play with.

Host workTunnel
    Host ssh.domain.com
    Port 5001
    # SMTP Server
    LocalForward localhost:2525 smtp.domain.com:25
    # Corporate Wiki.  Using IP address to show that you can.
    LocalForward localhost:8080 192.168.0.110:8080
    # IMAP Mail Server
    LocalForward locahost:1430  imap.pretendco.com:143
    # Subversion Server
    LocalForward locahost:2222  svn.pretendco.com:22
    # NFS Server
    LocalForward locahost:2049  nfs.pretendco.com:2049
    # SMB/CIFS Server
    LocalForward locahost:3020  smb.pretendco.com:3020
    # SSH Server
    LocalForward locahost:2220  dev.pretendco.com:22
    # VNC Server
    LocalForward locahost:5900  dev.pretendco.com:5900

### Hostname aliases ###
### These allow you to mimic hostnames as they appear at work.
### Note that you don't need to use a FQDN; you can use a short name.
Host smtp.domain.com
    HostName localhost
    Port 2525
Host wiki.domain.com
    HostName localhost
    Port 8080
Host imap.domain.com
    HostName localhost
    Port 1430
Host svn.domain.com
    HostName localhost
    Port 2222
Host nfs.domain.com
    HostName localhost
    Port 2049
Host smb.domain.com
    HostName localhost
    Port 3020
Host dev.domain.com
    HostName localhost
    Port 2220
Host vnc.domain.com
    HostName localhost
    Port 5900