I don’t know about you, but my Mac is full of stuff. Files, PDFs, Word and Pages documents, Excel and Numbers spreadsheets, emails, notes, web clippings, movie files, images, outlines, databases and more. It’s incredible, but my main hard drive has about 350 GB of stuff on it and I only have a faint idea of what may be hiding deep down in the most distant crevices of my Mac.

And it gets more daily: Emails pop into my inbox, I download stuff from websites, I create new documents… if there’s one thing I can say for sure: the amount of data on my Mac is only going to grow over time, so I better start thinking about how to manage all this stuff more effectively.

With the number of files inhabiting my machine, managing them with the Finder in folder hierarchies is quickly becoming a hassle. Out of the box, Mac OS X just doesn’t have that many easily accessible ways of managing a large number of files. Tagging? Not really. You have the Spotlight comments field in the Get Info window, but that gets crammed quickly and there’s no way of browsing them either. Spotlight? It’s much more powerful than meets the eye, but using its query language isn’t everyone’s cup of tea.

So I did some research, looking for apps that would help me manage my collection of data easily and efficiently. I found lots of apps that let you take notes (which is much better than keeping your notes in individual files), embed numerous types of files and search and tag your data. I looked for well-supported apps, since I’m going to be trusting them with my precious data and I wouldn’t want to end up in a tight spot with some important documents in a database of an app, who’s developer has moved on to greater things.

Here’s an overview of the apps I came up with after researching and filtering, in no particular order.

Yep / Leap

Yep and Leap are actually two separate apps. The reason I mentiond them here together, is that, firstly, they work great together and, secondly, they are actually very similar in what they do.

Leap indexes all the files in your Home folder and initially adds tags based on existing metadata, the file name, its date and the folder it resides in. You can then add your own tags which are stored either in the file’s Spotlight comments or in Leap’s database.

When you’re in search of a specific file, you can enter search criteria and Leap filters down the files in real time. You can also limit the search to certain file types (e.g. PDFs, bookmarks or image files). Leap’s browser shows thumbnails of the files it finds, which, in my opinion, is a much better way of presenting a large number of files than Coverflow.

Yep is an indexing and tagging application that is specialized on PDF files. The developer calls Yep “iTunes for PDFs”, which describes Yep quite accurately.

On launch, Yep scans your hard drive for PDF documents and tags them (similarly to Leap) based on the folder they are located in, the file name and any existing Spotlight comments. You can then add your own tags. In many ways, Yep is like a PDF-only version of Leap. Here’s where it differs, though: Yep supports scanning and automatic archiving of documents. For example, if you happen to own the incredibly cool Fujitsu ScanSnap S510M, you can scan and archive documents simply by pushing the scanner’s scan button. Yep can be configured to import scanned documents automatically where you can then tag them and, if you wish, move them from the default scanner inbox folder to your preferred folder.

Overall, both Yep and Leap are a fresh new way of managing your files. Leap is more versatile in that it supports more than just PDFs. But Yep has scanner support. So if you’re trying to go paperless, you might want to check out both.

Yep will run you 34 USD, Leap costs 59 USD. You can get both for 69 USD bundled with Deep, which is sort of like Yep, but for images.

DEVONthink

Devon Technologies just released the public beta of DEVONthink 2.0, the long awaited successor to DEVONthink 1.x. DEVONthink stores documents, scanned papers, email messages, notes, bookmarks, web clippings and more in a database that can then be searched with a unique and very powerful artificial intelligence system. You can interlink items inside a DEVONthink database, view live web pages directly inside DEVONthink, use AppleScript to automate features, organize your database with smart groups and more.

DEVONthink Pro Office, just like Yep, integrates nicely with the Fujitsu ScanSnap S510M and can turn scanned documents into searchable text via OCR. It can also archive your emails and you can publish your DEVONthink database on the Web.

DEVONthink Pro / Pro Office is the most powerful of all the applications. Its artificial intelligence search engine is especially useful for finding things in large databases and often digs up stuff you completely forgot about. DEVONthink Pro Office (DTPO) also offers the most features, including document scanning and OCR and email archiving. No other application is as powerful, albeit DTPO is quite expensive (final pricing still to be announced). If you want or need an app that can handle literally all your data, you should give DTPO a serious look.

The official release of DEVONthink 2.0 is scheduled for early 2009. But you can already upgrade to version 2.0 if you own any previous versions of DEVONthink products.

EagleFiler

EagleFiler from C-Command software is another app for archiving email, web pages, PDFs and basically any file on your Mac. You can import files with a single keypress and then add tags, notes and labels.

Files aren’t actually imported into a database, but rather kept in their native format inside a specific folder structure so they stay accessible for other applications and there’s no need to export them, should you decide to move them to another app.

After importing data, you can browse the database very quickly using a number of criteria. You can create smart folders that work similar to smart folders in Finder, too.

EagleFiler is technically sophisticated and very robust and powerful. The only downside is that its interface is fairly Mac-unlike with all its separate windows and palettes. But if you want to archive your emails, EaglerFiler is the only other app besides DEVONthink Pro Office in this comparison that has that feature.

EagleFiler is available as a free 30-day trial, registration of the full version costs 40 USD.

Together (Keep It)

Together from Reinvented Software was previously called KIT. (Keep It Together) and now requires Mac OS X Leopard. You can put text, documents, images, movies, sounds, web pages and bookmarks into Together and then tag, label and organize them into folders and groups.

Importing is done either by dragging items directly onto the main window or onto the “Shelf”, the latter of which can be kept neatly tucked away at one of the screen edges and popped up whenever needed. You can open multiple items in tabs and view common formats with QuickLook.

Browsing the Together database is done either by searching, with the tag browser or by smart folders. Together also supports AppleScript and can sync data via MobileMe.

Together is my personal favorite among the dedicated data collection apps. Its interface is beautiful and you get more features than with any other application in its price range.

Together is available as a 15-day free trial, the full version costs 39 USD. Upgrades from KIT are available for 14.95 USD.

Yojimbo

Bare Bones Software’s Yojimbo can handle text, bookmarks, PDF files, web archives, serial numbers, passwords, and images and syncs its data via MobileMe, if you want to access your data from different locations.

You can organize your items with (smart) collections, encrypt sensitive data, use the Quick Input to add items on the fly, add items via drag and drop to the Dock, Yojimbo’s window or its “drop dock”, which hides at one side of your screen and appears when you drag an item onto it.

Yojimbo is similar in functionality to Together, except for nested folders, which it lacks. Its Quick Input window is the most versatile, allowing you to quickly choose what type of info you want to add to the database. Yojimbo costs exactly the same as Together, so it’s basically a matter of taste which one works better for you.

You can try the 30-day free trial version and, if you decide that Yojimbo is for you, purchase the full version for 39 USD. Educational pricing and a family pack are available for 29 USD and 69 USD, respectively.

Shovebox

ShoveBox is the most basic of all the apps reviewed here. For example, it doesn’t have the ability to nest folders and you can’t use tags. But you can label or flag items, create text notes and import from your iSight.

Capturing data is done by drag and drop to the system menu item. Imported data can be automatically sorted by user-definable rules and “QuickJot” lets you quickly enter a note into the app without having to switch to it first.

ShoveBox is the most basic app of all in this comparison. The importing of data via the system menu item is unique, but has the advantage that it’s easily accessible from any app. But ShoveBox lacks nested and smart folders and some other features, which makes it the choice for only the most basic needs.

ShoveBox is available as a free trial version, the full version costs 24.95 USD.

Conclusion

Which of these apps you choose for organizing your data is first and foremost a question of what you need. If you need archiving of emails, you’re best off with either DEVONthink Pro Office or EagleFiler. DEVONthink Pro, Together and Yojimbo are all versatile, stable and easy to use and feature similar functionality, with DEVONthink offering the most sophisticated search engine and the ability to store your data in multiple databases. For a simple and lightweight solution for dropping all your stuff into, check out ShoveBox. And if you just want a convenient way of browsing your existing files and folders, give Leap and/or Yep a try.