Compression software falls into roughly 4 groups based on the intended users.
Type 1 - This is the 'we do it all for you' software. This type usually costs between $20 and $100. With this type of software, all you usually set is bitrate, output size, path and filename. This type of software is sold (often for a very low price) to people who don't want to know anything about compression. There is little incentive for the authors to optimize quality, so quality generally suffers. This type of software generally uses cheaper, lower quality codecs. Since there are so few options, this type of software is generally very easy to use.
Type 2 - This type is a step up from Type 1. This type usually costs between $50 and $200. This type gives you some settings like 2 pass encoding, CBR/VBR encoding, and so forth, but doesn't give you a lot of settings. This type of software is aimed at people who have to deliver compressed output, but who don't compress as a primary task (video editors, producers, and so forth), but who care somewhat about quality and file size. The quality of this type of software is generally better than Type 1, but cannot be tweaked very much. Any presets provided are generally fairly good. This type of software generally uses moderately priced, good quality codecs. Ease of use is still an important selling point, so this type is generally fairly easy to use. Adobe Media Encoder and Compressor fall into this type.
Type 3 - This type is the software generally used by compression experts. This type usually costs between $200 and $1,000. This type gives you a lot of settings for every type of compression, comes with a lot of pretty good presets, and includes functions for related tasks like deinterlacing, reverse telecine, noise reduction, batch processing, etc. Since output quality is the primary selling point of this type of software, you can get very high quality. This type of software generally uses higher priced, very good quality codecs, and may offer a choice of codecs for the same output format. On the flip side, since there are so many options, and since ease of use is at best secondary, this type of software is generally hard to use, although there are exceptions. Telestream Episode and Sorenson Squeeze are this type.
Type 4 - This is the 'we give you enough rope to hang yourself' type. This type usually costs more than $1,000. This type is usually aimed towards high-volume production companies that need a render farm to output massive quantities of compressed video. You can change any imaginable setting of each supported type of compression, and there are features to support many types of workflow. Since you can adjust all parameters, you can get excellent results if (and only if) you know what to set. This type of software generally offers the best codecs. This type of software is generally designed to be set up by someone who knows a lot about compression, and generally is very hard to use outside of using already set up workflows. Some examples of this type are Rhozet Carbon Coder, Inlet Fathom, and Telestream Flip Factory.
Note that these are general categories, and not meant to be exclusive. Some software may fall between categories, or may fit into more than one category.
Of special note is ffmpeg and x264, which fall into type 4 in options, quality and difficulty to use, but is available for free. There are front ends for ffmpeg, which generally fall into types 1 or 2.