The cut down ones were on the DVDs (reduced from about 45 mins to about 25 on average) of the RTD era. Not sure if they're on the modern prints, but those cut downs are on the original UK DVDs at least.
The Moffat era episodes are entirely MIA.
There's loads missing, tbh. Like the RTD era did two commentaries for every episode - a DVD commentary, but also a podcast released online immediately after the episode aired. There's a fucking incredible one with Moffat, RTD and Tennant recorded literally a week after Moffat taking over was announced, and it has those two relentlessly ripping into him (in a friendly way) about all of the rumors of things he'd have coming back and do with the show. Some of those commentaries are gold, others really fascinating, and the BBC website has just swallowed them up.
Most of the most significant episodes of DWM are available online in their original format in dodgy forms, just usually you have to search for the episode number. Here's the one you're after:
https://www.dailymotion.com/video/x6t3g1f