I currently use winscp.
You'll want to use this as your info and ssh in:
Hostname: Your iPhones IP address - it needs to be on your internet network (use the network address 192.xxx.x.xx or plugged into your computer using the data ip address).
I would suggest changing that default password after this if you haven't done so. If you use the Rock crack store, it should allow you to change it the first time you log in.
IF you are not used to SSHing, I believe for system sounds, you can just use Iphone Explorer which is free as well instead of SSH and WinSCP. You need to go to Rock or Cydia and install "afc2add" though, this will allow you to reach the root on a 3Gs phone using Iphone Explorer.
Then- back to common instructions:
Go to this directory:
Make a backup of it and store it somewhere safe. You'll be replacing these files.
Then, I like Switch sound file converter, you need to change the sounds you want to use to .aiff format. Then, rename the file to a .caf file using the original name of the file you want to replace.
For example: I use the NCIS theme song for incoming text messages so I changed my NCIS.aiff to sms-received4.caf. Also I sometimes use the transformers transforming sound for my unlock sound so I changed tf.aiff to lock.caf.
Then I copied these files to the directory above replacing the old files. You may have to respring but after you do that, viola! You have customized sounds!
I hope this was helpful, take care, backup, and share the info with someone if they need it.
The net should be a free, open, helpful society as an ideal world. It isn't but we can help.
Have a good one!
Btw, this was an aggregation of many sites I have read in the past and I give full credit to those who had done this before me. I needed to compile the info into one easy to read instruction sheet though so that's what this is. I hope it's as easy to use as I think it is. Feel free to copy and save it.