Time Machine backups to a Linux machine running Netatalk is a very convenient way of safeguarding your data. However, the I/O load on the server machine can sometimes become very high. Here is a quick hack to improve this, if you need AppleTalk AFP services mostly for TimeMachine.
The fastest and easiest way on Ubuntu 12.04 LTS is to add the following line to /etc/default/netatalk on the Linux server and restart Netatalk thereafter with /etc/init.d/netatalk restart:
renice -20 $$
This gives the Netatalk processes the lowest CPU priority. On recent Linux systems, this also reduces the I/O priority of these processes. If you run anything else (web server, mail server, webmail, ownCloud, …) on the machine, they will have both CPU and I/O priority.
If your server is heavily loaded, your backups will take longer, but most users will gladly accept this if their more interactive services react faster.