The /src file is obviously designed to contain source code, so when I download programs, I should put them in /src (because they contain the source files + the executables)? What do most people do with the executables? Do they copy them to /bin, make links to them in /bin, or just leave them in /src? I am new to Linux, but I would like to start doing this correctly. Thanks!

If you download something, best place it somewhere, where no one accidentally uses it, deletes it or something.

/src is no file but a directory and it is no standard directory on every Unix/Linux.

Depending on what you downloaded, source code, binaries, whatever, you'll have to read the docu for it, before you start putting them somewhere in the filesystem. Many program packages use either the built in package handler of your OS, like rpm or whatever.
Some others that come as source code often have to be configured to your needs, and then compiled using "make".
This info is a very general overview. You have to read the docu if you are unsure what to do next after download.

I'd go even further, and recommend that as a regular user, you simply keep stuff in your home directory, and let the designated system administration interface (dpkg or rpm if you're on Debian or Red Hat, respectively) deal with the rest of the disk.

Hi, thanks for the replies. I'll try to be more specific because I think my first post was quite vague. Sorry.

In my home directory, I have the folders ~/bin and ~/src. When I compile a program such as BLAST from source code, it seems that I should keep the BLAST folder in the ~/src directory because it contains the program's source code. Within the BLAST directory, there is a ./bin folder that contains the executables. I was simply wondering -- is it common practice to move these to my ~/bin directory, to make links to them in my ~/bin directory, or to just keep them in my ~/src directory and to execute them from there? If the answer to this question varies depending on the program, I'll just try to do whatever seems best. It is not very important, but I was just curious what the standard practice is in the Unix world. Thanks!

Common practice is that after you do

configure
make
make install