Because there ARE so many wonderful downloads available, I highly recommend sorting your downloads, and only having certain THEMED downloads installed in your game at any given time. For instance, if you're working on a Winter-themed zoo, only have Winter and Christmas-themed downloads installed while you're working on that zoo. Keep the other ztd files in a Temporary ZT folder (name of your choice - I use "Updates Temp"), and simply swap them out when you're ready to do a new zoo. Keep in mind, though, that every time you change the contents of your Updates (or dlupdates) folder, you will need to restart the Zoo Tycoon game so that it will recognize the new items.
If you happen to get into forum contests, I also recommend changing the file name prior to placing them in your updates or dlupdates folder. As most forums will say, "Zoo Admin downloads only (for example)", you'll need to keep them sorted by site, as well as type. Some people make separate folders, but it can get confusing if you're wanting to use downloads from several different sites for a zoo you're doing. What I do is rename all my downloads by site: ie. "gcSecretGardenPack.ztd" becomes "ZtekSecretGardenPack.ztd" or "ZtekgcSecretGardenPack.ztd", "gcChocoPath.ztd" becomes "ZTUFChocoPath.ztd", "gcTarPath.ztd" becomes "ZATarPath.ztd", and so on. (They all have "gc" at the beginning because the downloads I made are the only ones I can remember off the top of my head
) Renaming them this way will allow you to sort them by site in a matter of seconds, and is a HUGE help when you get involved in "THIS site only" contests