Get Artwork and Metadata: Video
Now that you've converted your videos, a handy program called MetaX (version 2.25, $10) can spare you the trouble of manually adding the titles and tags for the converted files. Associating titles and tags with your video files (and audio) will enable you to find, preview, and sort videos on your desktop or iOS device easily.
MetaX does all the hard work for you, including searching online movie databases (by matching the video title) and populating the file with descriptions, crew and cast members. MetaX also pulls high-res movie posters, so your video collection will look great in CoverFlow or in the Videos app on iPhone, iPads, and AppleTV.
Get Artwork and Metadata: Audio
MetaX works only with MP4 and derivative video files (such as files converted by HandBrake). To import missing artwork for your albums into iTunes, you have a couple of options. The first, a built-in iTunes feature in the Advanced menu called Get Album Artwork, works if you've correctly tagged the albums and artist fields. Unfortunately, iTunes probably won't find artwork for obscure artists, but if you have only a few songs missing their metadata, you can add them manually quite easily.
iTunes' automatic artwork download feature works only if you have an Apple ID account. If for some reason you don't want to go this route, consider using CopyTrans TuneTastic, a free (beta for now) utility that can clean up your audio archive. TuneTastic scans your iTunes library to locate unidentifiable songs (with exclamation marks), delete duplicates tracks, and get missing artwork for your albums. Afterward, the files will be updated in iTunes, so you can view album art and song metadata in Apple's CoverFlow.
Manage Files on iOS
There are a few ways to circumvent Apple's iTunes lockdown without having to jailbreak your iPhone, iPad, or iPod. If you want to transfer music and other files from an iPhone to any PC, a program called CopyTrans ($20) will let you.
CopyTrans transfers iPhone music, videos, and ringtones directly to iTunes--so you can easily populate your iTunes library on a new computer, for example. The utility scans your phone, detects which songs you already have on your PC, and then prompts you to copy the rest. This is a handy tool for dumping multimedia content from your iOS device without being forced to authorize your iPhone or iPad with Apple's iTunes on your desktop.