Hi,
I'm using DIY Layout Creator (Windows only!) to be found here: -software.co.yu/diy/index.php?project=software
Even though the original intention of the author was to create a tool for small audio projects, it is also fine for small µC-projects.
Its a bit slow in some of the functions like moving and selecting parts.
On the other hand it is freeware (sadly not open source, it would really need some performance optimization)
Another commercial tool can be found here: -online.de/uk/html/lochmaster.html
But this one is for stripboards. Maybe it supports perfboards too? Give it a try, because they have a demo in the download section.