As the Pioneer decks can handle CD audio, MP3, AAC, AIFF and WAV, those will be the file formats we'll be focusing on here. While some programs can handle other formats, those will simply be a bonus for you.
This list is by no means a full compilation of what's available, but rather those we've tested and found to be useful.
Post last updated: Feb. 2nd, 2010
MP3 Error Checkers / Validators
MP3val (Free) One of the best utilities for detecting and correcting errors in your MP3s.
MP3 Checker (Free) It's a few years old, but it also scans for corruption in your MP3s. I should note that I haven't had this one find anything that MP3val couldn't... but several slipped past here that MP3val caught.
MP3 Scan+Repair (Free) This is the best (and one of the only) MP3 validators for the Mac. Does a fantastic job and it tells you what's wrong!
MP3-Check (Free) Allows you to set parameters to check your MP3s for ID3, bit rate, sample rate, channel mode and gain volume. This program does not check for errors, but would assist you in finding any low-bitrate MP3s (for example).
EncSpot (Free) A great simple program for providing information about the encoder used on your MP3s. Also provides other basic file details including the bit rate, sample rate, channel mode. Does not detect errors.
MediaInfo (Free) Provides detailed information about virtually any media file. Also displays parameters used at time of encoding.
MP3-Info (Free) Works as a plugin for Finder and iTunes to provide additional information about the track including bit rate, etc.
WinMP3Packer (Free) Useful for converting VBR MP3 files to CBR files without running any re-encoding. It basically pads the file to make it a CBR without adding any additional filesize. This is an updated link with the GUI information; scroll to the bottom of the page and click the link to download WinMP3Packer, not MP3Packer.
MP3Packer (Free) Same as above, just a re-packaged OSX version.
Tag & Rename ($30) Hands-down the best ID3 editor I've used on the Windows platform (and better than anything I've used on Mac too, for that matter). The flexibility of the program is so incredible it's just worth getting based on my praise alone rather than me going into detail about what it can do. Batch editing, seek + replace, conditional highlighting ... it's so worth the $30.
MetatOGGer (Free) As the name implies, it supports OGG files, but does a decent job of displaying and handling all sorts of ID3 information. Not as powerful as Tag & Rename, but it's simple and free.
The Ultimate Tagscanner (Free) A very powerful ID3 editor which can do virtually anything you could ever imagine you need to do with tags and filenames, just takes a bit of learning the difficult interface to use. Thanks RyanJ!
MP3tag (Free) Another free ID3 editor for a variety of file formats. Nothing wrong with another option! Thanks Azu!
PC & Mac
Jaikoz Audio Tagger (£15) This app is pretty encompassing and can handle all your major tag editing needs for multiple file formats. Jaikoz has MusicBrainz embedded so it can use acoustic fingerprinting to lookup tags (although I've not really had any success in my tests, maybe it's because I'm using obscure music). It is cross platform (they offer Windows, Mac and Linux flavours), but in terms of power, I don't feel it matches Tag & Rename, even with the MusicBrainz features.
Musorg (Free) A simple free app for editing ID3 tags. Doesn't support embedded art. Where it beats the pants off of iTunes is the ability for it to rename files based on the ID3 tags.
Ripping & Encoding
Easy CD-DA Extractor (€25 / $38) I love this program, I've been using it for years. Not only does it rip CDs to any number of audio formats, but it also cross-converts AND burns! Yeah, you could use iTunes, but 15 million downloads on CNet can't be wrong.
Free Rip (Free / $30 for Pro) This program seems to do a decent job for a freebie, so I'm also offering it up for people to check out. It also cross-converts audio files.
Audion (Free) A simple app for ripping and encoding. It's no longer in production and thus they're offering it for free.
Nero ($70) Nero is one of the essential PC apps because it does SO MUCH... (CDs, DVDs, ripping, encoding audio and video, etc) but if you need it to do a bit less, you can always get their free version which still allows you to burn and copy CDs.
CDBurnerXP (Free) Don't let the name fool you, it works on Vista and W7 as well. It's a fantastic program and will handle burning of most audio and data CDs you'll ever need, including ISOs. This is my free app of choice for burning, even if it can't handle the DVD creation / duplication / conversion the same way Nero can.
Toast ($80) Yeah, it does everything Nero does, but on a Mac. Fantastic program, another must-have.
Burn (Free) If you like to burn your toast, this is the freebie to get. Worth checking out if you don't want to spring the $80 for Toast, doesn't let you do some of the cool encoding and crosscoding video stuff Toast can handle.
Drive Formatting Utilities
HP USB Disk Storage Formatting Tool (Free) For some reason or another, the built-in Windows formatting tool does a piss-poor job of formatting things in FAT32 (when it lets you). This HP tool is fantastic for any version of Windows to format flash drives and hard drives to FAT32. Always remember to double-format! Again, we're not sure why but we just know that it's important to format your drive not once but twice with this utility.
FAT32format (Free) For users who have had an error using the HP tool above, try this utility by Ridgecrop Consultants. A couple of users have had success with it after being faced with error messages when connecting their USB drives to the CDJs.
Swiss Knife Premium (Trial / Pay) It's free to try ... and format your drive, which is all you'll really need it for. It's a proven success for DJs who have had problems with the HP formatting utility above.
Disk Utilities (Free - built in to OSX) OSX has this feature built-in for formatting drives, just go to Applications > Utilities > Disk Utility. From there you can select which drive to format, then click the Erase tab up top of the right screen, then select the Volume Format as either MS-DOS(FAT) or HFS+ (which will also work with Pioneer products).
Boot Record / Partition Repair Utilities
TestDisk (Free) This utility will repair a drive that can't be loaded, lost a partition or has the message "This drive is not formatted" thanks to a bad boot records. It's a very easy utility and certainly one worth noting... but still, nothing beats a back-up! Always back-up your data, especially if it's used for work (DJing).