Basically, the default install of Cleaner 6 is limited in what comparable quality you can achieve today. For Quicktime output with Cleaner, you probably want to use Sorenson Video 3, and you would want to use the Pro version of the encoder which can offer 2-pass and VBR encoding ($299). For Windows Media from Cleaner, you would want to use the encoder from Flip4Mac, which can encode to WMV-9 and offers 2-pass and VBR too ($179). There is also a WMV encoder from Popwire which offers single pass VBR encoding, and quality can be quite good as well for most sources ($29).
If the thought of spending that much to just update a dying app (Cleaner) unsettles you, then the other options are to look into a new compression suite. Sorenson Squeeze 4.1 comes with the SV3 Pro encoder, but you still have to purchase the Flip4Mac plugin to encode Windows Media ($399+$179=$578). Another compression suite, Compression Master 3.1 from Popwire, offers 2-pass VBR WMV-9 encoding, and 2-pass VBR MPEG-4 QT-compatible encoding, which is very nearly just as high quality as SV3, for a reasonable price ($399). CM 3.1 also has the most extensive set of presets for easily being able to produce quality output for beginners.