Where is the recommended place to install applications that are not from apt

The place for this is in /opt for "Add-on application software packages" - these are packages that do not come with the distribution/OS.

http://www.pathname.com/fhs/pub/fhs-2.3.html#OPTADDONAPPLICATIONSOFTWAREPACKAGES

There is a difference between /opt and /usr/local/bin. So just symlinking binaries from one to another would be confusing. I would not mix them up.

/opt is for the installation of add-on application software packages, whereas the /usr/local directory is for the system administrator when installing software locally (with make and make install). /usr/local/bin is intended for binaries from software installed under /usr/local.

According to the File Hierarchy Standard, the correct way would be to add /opt/<package>/bin to the $PATH for each individual package. If this is too painful (when you have an uncountable number of /opt/<package>/bin direcories for example) then you (the local administrator) can create symlinks from /opt/<package>/bin to the /opt/bin directory. This can then be added to the users $PATH once.