Android Folder Hierarchy

First, you need to be aware of two facts:

• Android uses more than one file system (think of "multiple drives/partitions" when comparing with your computer
• while sharing a common base, directory structures might differ between manufacturers

So as starting points, I further recommend the file-system tag-wiki and the partition tag-wiki (you might also want to take a look at the most frequented questions using those tags).

In my answer, I will concentrate on the mentioned "common base". However, there still might be deviations made by some manufacturers.

Partitions

As said, Android makes use of multiple partitions. In the file system, they are represented by "directories", which serve as their mount-points:

¹ Details below
² virtual file systems
³ these might differ. Often, /mnt/sdcard is the internal SD card, while the external SD card is found in /mnt/sdcard/external_sd.

Above list is far from being complete, but should hold the most important partitions.

Directories

Here I again will concentrate on the partitions which are most interesting (or this answer would get far too long and, for most readers, boring.

/data and /data/data

These are in most cases two separate partitions, but there might be cases where this is handled otherwise. One thing they have in common (add /cache here as well): they get wiped on a factory-reset, while the other partitions are usually left untouched by that.

As for the directories contained, I will again concentrate on a selection; most things here you either cannot touch without having your device rooted.

¹ for details on the Dalvik cache, see: dalvik
² each app gets its own data directory assigned here, using the app's package name. There might be a similar directory on your SD card, mostly used by apps with larger amounts of data.
³ usually, files are stored here temporarily to be installed/executed. Google Play e.g. downloads .apk files to this directory, before installing the downloaded app on your device

Of course, I intentionally skipped several directories. If you really want to go into details, this site might not be the best fitting place (as we deal with end-user questions -- and end-users normally don't touch these things). In that case, several places/resources might be recommended:

• XDA Developers
• good technical books on Android (e.g. Andrew Hoog's Android Forensics and Mobile Security, which goes much deeper into details here)
• Where can I ask questions that aren't Android Enthusiast questions?