I know where some files belong but I keep coming across new files that I don't know what folder to place them in. This is what I already know. 

.cr2 is a figure (Folder: Character) 

.pp2 is a prop (Folder: Props) 

.pz2 is a pose (Folder: Pose) 

.lt2 is a light set (Folder: Lights) 

.fc2 is a face (expression) (Folder: Face) 

.obj is geometry (Folder: Geometries) 

I have also come across file types which I'm not sure what they are for and where they belong. 

Some examples are: 

.uvs 

.mc6 

.hr2 

.hd2

.rsr 

.cm2

.pz3

.jpg and .png files (Do these go in the materials folder? How are they used?)

I need a more comprehensive guide to help me place different files in the right folders.  

.uvs - not directly used by Poser

.mc6 - Material Collection - goes in Materials

.hr2 - Hair (non conforming AKA Prop Hair) - goes in Hair (Conforming Hair goes in Figures)

.hd2 - Hand - goes in Hands (edited to correct a very silly error)

.rsr - Resource file - no longer used

.cm2 - Camera - goes in Cameras

.pz3 - Poser scene file - best put somewhere away from Poser, unless you want a ridiculously huge Runtime.

.jpg and .png - Image files - go into Textures

If you're unzipping stuff, it's always best to note the folder structure of the zip and use that, since Poser will look for files to be in the places it assumes them to be.  For example, if you unzip one of my Dalek freebies, the obj goes in Runtime/Geometries/SamTherapy, the Material Collections go in Runtime/Libraries/Materials/Daleks (or similar).

You can set Winzip - or 7Zip (much, much better) to unzip to the correct locations in Poser.  As you get more adept, you can customize the folders to your own preference but for now, I suggest you leave it vanilla.  

The only addendum I'd make there is that sometimes .rsr or .png files can be the thumbnails for the other Poser file formats;

e.g. if you have a "figure.cr2" file you might have a "figure.png" thumbnail sitting alongside it.

I've found a few freebies... and even older marketplace products that still have .rsr files for the thumbnails... and had to convert these to .png format, so that the thumbnails would show up in my Poser Library, on my mac.

Are there any other files used by Poser that I have not mentioned above? 

I don't think you mentioned .mc5?

.mc6 is a group shaders, for several material zones (the material zone names in the .mc6 have to match up with the zone names in the figure or prop you're applying the mat to).

.mc5 is a single shader, for a single zone (can be applied to any zone).

.mt5 is for a single zone shader

Also to be noted, the final number in a file extension will be replaced by a "z" if the file is in a compressed form (e.g., cr2 becomes crz)

Whoops, sorry... yes, I meant .mt5, NOT .mc5

To add to what others have already written.......

If you are running Poser9/2012 you could put these anywhere - I don't recommend that however - you will lose stuff.

Use the standard runtime structure - when you get a bloated runtime (and you will) following the file structure will save you anguish later.  Spend time now thinking about how you want your Runtime structure set up - Don't be like me - restructuring your 300GB worth of runtimes are no fun at all......

.pz3 files go in the Scene folder - more than likely, it won't have a .png file to go with it - you can very easily create one.  You know you are going to load it and render it at least once, go ahead and save the render & resize it to 91 x 91 png and save it to the Scene folder (use same name as the .pz3).

.pz2 files can be either a material or a pose (This is a legacy from Poser 4 - since DAZ set their compatibility at Poser 4, way too many Poser vendors are still making only material .pz2s.)  The good news is that there is a niftly little program called Batch Material Convert by Netherworks Studio that will convert your material pz2 files to mc6 files and put them in the Materials folder - The Poser standard since Poser 6.  I can't recommend it enough - I converted a 40+GB V4 clothing runtime in less than 30 seconds (4 clicks).  Is is available here at renderosity:

http://www.renderosity.com/mod/bcs/batch-material-convert/89330

You may also run into some strange folders that hang out in the library folder that aren't part of the standard Poser file structure.

These are morph .pz2 files that should NOT be messed with by the end user (they are called by other .pz2 files) - you can recognize them by the name of the file - they will have one of the four terms in their name: Hide, InjDeltas, RemDeltas, or Unhide.  They may or may not (Vendor's Call) reside in a subfolder called ChanVis (Hide, Unhide) or Deltas (InjDeltas, RemDeltas).

As an example, all of these for DAZ figures (V3, V4, M3, M4, etc) are in a file folder called !DAZ, Handspan Studios use !HSS, Billy-T uses !BILLY-T. 

In Poser 9/2012, SM has added a folder called Morphs.  They can be placed in there (Most people don't - I do) - the up side is they are all in one place - the down side is that most of the files in these folders are hard-coded and don't recognize the Morphs folder - as an example (a line from the InjDeltas.Aiko4All_ON.pz2):

readScript ":Runtime:libraries:!DAZ:Victoria 4:Deltas:Aiko 4:InjDeltas.PHMA4LashesGone.pz2"

So if I loaded INJ Aiko V4 into V4, Poser will ask me where the InjDeltas.Aiko4All_ON.pz2 is because the Morphs folder isn't in the readScript line.  I am willing to put up with this to keep my runtimes neat. 

It would really be nice, if in the future, Vendors would actually take advantage of this - I am not holding my breath on it though - Poser vendors are very, very, very reluctant to leave Poser 4 and DOS naming conventions behind.

.jpg and .png files can go in several places depending on what they represent.  Every .cr2, pz2, etc should have a thumbnail that will show up in poser - it is a .png file (older products will have an .rsr file - Starting with Poser 8/2010, Poser will no longer read them - they must be converted to a .png file  There are several products available to do that - I use RSRConv (OSX):

http://braintrigger.com/

There is a product that does the same for Windows here:

http://neocron.webspaceforme.net/alforum/index.php?topic=1489.0

These pngs are small files (usually 20k or so)

jpgs & pngs are also used as textures - these can be quite large (up to a few Megabytes)  These provide the textures for for your characters and models.  They go in the Textures folder. The normal convention is that like the files in the Geometries folder: the top folder is the vendor name - item name subfolder - jpg & png files.  Needless to say, not every vendor does this - If I have a product that doesn't follow this, I change it.  It only takes a second and it makes it easy to scan a Texture folder or Geometries folder and see who made what.

.lt2 - lights  fc2 - face (expression) and there is a dyn for cloth or hair dynamics.  and of course the dreaded pmd for external binary morphs.

all the poser file types have the compressed version if you turn on use compressed files in general preferences.  They have a z in them so pz2 becomes p2z, cr2 is crz etc.

I don't run across many stray files unless its say textures but what I find is stuff either comes as a runtime in a zip file or the stuff from Daz is exes which you just point it right to your runtime. In the zips I just drag and drop and overwrite my real runtime I use with the one in the zip and it adds everything nice and neat and you don't have to worry about it deleting. Its hard to get use to doing that till you do it awhile then it comes easy and everything is where it should be and should be available to you in poser. I find sometimes I have to explore those zipped runtimes and get folder names to search for to help me find it in the poser search engine.

Quote - I've found a few freebies... and even older marketplace products that still have .rsr files for the thumbnails... and had to convert these to .png format, so that the thumbnails would show up in my Poser Library, on my mac.

This is what I use to convert (in Windows) .rsr files to .PNGs that modern versions of Poser can use...

http://neocron.webspaceforme.net/alforum/index.php?topic=1489.0

Googling will turn up a Mac equivalent...

Quote - I don't run across many stray files unless its say textures but what I find is stuff either comes as a runtime in a zip file or the stuff from Daz is exes which you just point it right to your runtime. In the zips I just drag and drop and overwrite my real runtime I use with the one in the zip and it adds everything nice and neat and you don't have to worry about it deleting. Its hard to get use to doing that till you do it awhile then it comes easy and everything is where it should be and should be available to you in poser. I find sometimes I have to explore those zipped runtimes and get folder names to search for to help me find it in the poser search engine.  

To clarify on the Daz3d install exes, I think its you just point to the folder your runtime is in i.e. Poser Pro 2012 and not actually in or the root of the runtime folder itself.

Thank you all! This is useful information.