I am wondering if there is a way to organize content in Poser 11 without messing with the actual files?  I don't want to mess with the files themselves but a way to help find stuff easier.

Unfortunately, the only way would be to move the files themselves. 

If there are things you use frequently, you can add them to your favorites. You won’t need to move the file and you can put figures, poses, props etc all in the same folder 

The favorites folders allows you to organize you content however you like. Select any content and click the star icon at the bottom of the library. That will allow you to add that item to an existing favorites folder or create a new one. All your favorites are available in the favorites category of the library. Favorites can be drag n' dropped inside the Favorites folders.

Can you let us know what types of things you are trying to organize? Like if you wanted to separate all the V4 clothing from the V4 character/texture from the M4 stuff, you might want to consider having an external runtimes folder for each.  For example, I have on my program files folder a folder called "external runtimes". Under that folder I have separate folders for V4 clothing, V4 hair, V4 characters, M4 clothing, M4 characters, Props and Scenes, Animals, Creatures.  When I unzip a V4 character, I extract all the contents to the external runtimes/V4 Characters folder.  After you have all your separate runtimes, you can load each runtime in poser library and just switch between them.

The favorites option isn't a bad one, I just wish you could point to an entire folder you like rather than load each piece one by one. There has been some discussion on this entire folder pointing, but it's tricky.  I wish they would upgrade the favorites options.

The Favorites folders option is convenient when you want to access regularly used content from different Library Runtimes.  But you need to realize that, if you examine the Favorites folder, the contents are actually shortcut linked and the icons are duplicates of the originals.  I can understand why you need to add each item separately to the Favorites folder within the Poser Library, it would prevent locking up the program, or crashing if you attempt to add a folder.  You could manually add folders externally through the browser, however that defeats the purpose of a Favorites folder if you add all your content to it especially if it is content that is seldom or not used at all.

External libraries ?

I've a vast zoo of 'stuff' from lo-poly 3DS props dating back to ~2002, pre-P3, all the way to today's trawl. I put only essentials into Poser's internal library. The rest is sorta-organised into folder trees on my archive drives. If necessary, I'll link an external run-time, un-link when notion resolved. Usually, I just import files, save render, notes and PZ3 to source folder...

I know the OP doesn't want to have to move files in the library, but for anyone else looking for ideas for how to organize their Poser content, you might find it helpful to know that you can organize files inside the main Libraries folders pretty much any way you want, with a few limitations. Because this topic comes up a lot, as does the topic of "how many runtimes do you use," I finally wrote a piece on my blog to show how I've extensively organized all my content using only one runtime. If you're curious, you can check it out here: Organizing Poser Assets.

Using multiple runtimes drove me nuts, esp. for items that could plausibly be in more than one runtime, so I found it easier to just use sub-folders within the main Libraries folders to organize by figure or genre or whatever. Makes it easy to find things AND easy to install them (which I always do manually.)

As for using the Favorites option in Poser's library, be aware that it's creating shortcuts with full path references, so if you end up moving an item a shortcut points to to a different folder, the shortcut will break. Given my propensity for moving things around, I don't use Favorites.