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Before noticing it, you may end up with hundreds of soundfont files, especially if you have a broadband internet connection and a very picky ear. Indirectly, the quality of your project can depend on how you organize your samples, as you may miss a good sample you actually have if the files are scattered (speaking from experience).

Organize by instrument. Look at how the 128 GM instruments are listed to get an idea. Make a folder for each instrument group. Libraries that contain a set of files may have their own folders (e.g.  DSK, Sonatina Symphonic Orchestra). GM/GS files (single file with all the 128 instruments packed together) should also go together in their designated folder. The sparse independent random samples are best organized by instrument group. Some files are not very intuitively named (e.g. named after the model number of the instrument, specially for drum kits and electric guitars).

It may not be a good idea to rename them as you might end up downloading them again (this really happens if the filename does not give you a clue of what instrument it is, tending to be unused and forgotten), and you may find forums and reviews talking about a specifically named soundfont.

Of course, the same applies for VSTi’s and VSTs when possible (some VSTs come in a setup program, while most others are just the bare DLLs).

One downside I realized is that some DAW software do not offer you the option to browse for soundfonts or VSTs, but instead scan a predefined directory (this directory may probably be changed in the Windows Registry). Audacity is an example. I think this is bad design. Some samples can be gigabytes in size and I would not like having them in my system partition (drive C:).

Where to look for soundfonts? Hammersound seems to be quite known and is nicely organized (websites are another source of organizing ideas). For files that can not be found in Hammersound, or if the link is broken, sf2midi might be the next best place, despite its many ads and the free registration required.