Although the series itself is available online if you know where to look, a considerable amount of media related to it is currently unavailable.
Found/Partially Found Media
The Nicktoons American dub (Partially Found)
Paired with "Wedgie Attack" in the second of the double-billed episodes in Nicktoons broadcasts, the episode "Bogie Ball" had every use of the word "bogie" redubbed into "booger" for all voice lines, and the title-card was changed accordingly. Edited portions of it were uploaded by YouTube User TheSecretShow4You from their own camrip, although in very low quality. (It has now been found in good quality from an unedited source via the link below)
Additionally, the episode "The Z-Ray Goggles Of Power" was redubbed to say "ZEE-Ray Goggles" instead of "ZED-Ray Goggles" when aired on Nicktoons.
It is unknown how many additional episodes were redubbed as only 1 TVrip of the 26 Nicktoons double-bills has surfaced - that being Dr. Hypno Returns Again / Secret Sleep, neither of which appear to have been modified - although on Nov 2nd, 2017, master copies were located for two further double bills, and as of the 23rd they have both been uploaded - the episodes in question being Booger Ball / Wedgie Attack,and Flick The Switch / Giant Brain Of Terror, bringing the total tally to 3/26 found.
The Martian Dub of "Super-Vic" (Found)
One of the most famous pieces of lost media from the show, this was exclusive to the Australian release of the Volume 2 DVD - although TV listings suggest it may have briefly aired on Nicktoons. It was a self-satirical in-character commentary on the episode "Super-Vic", showing the main cast supposedly "redubbing the episode into Martian for the benefit of those watching on Mars", seemingly on their first take. Naturally, the "Martian" is nonsense and the redub devolves into everyone arguing over what the Martian language supposedly is, and what actually happened during the episode's events. Remaining elusive for many years, it was found and uploaded onto Google Drive and shared on Tumblr in its entirety in late 2016.
Commentary on "Flick The Switch!" (Found)
Previously completely unheard of, this overdub was meant to have been released on the cancelled Volume 3 DVD, which never made it to market despite reportedly being complete. It was uploaded by an anonymous affiliate of Tony Collingwood to YouTube in late 2016 but was immediately blocked by the Content ID system, leaving it inaccessible before it caught any public attention.
According to Mr. Collingwood himself, “I enjoyed writing [The Martian Dub] – and we had a blast recording it with the actors. We did another episode like that as a DVD extra, where Changed Daily held a post-mission briefing, with the entire cast commenting on how they did during the episode. Not sure if that ever made it out into the world?”
As of Nov 23rd, 2017, the commentary has been found, and contains references to many parts of canon that until now had only been mentioned by the show staff but not stated in any episodes, such as "Ding Ba-Doo" meaning "Freeze The World", Changed Daily continually "seeing pink elephants" on-duty, and his preference for madeira cake. It is also revealed that it was Special Agent Ray who drew "the kaboom picture" and that the episode took place on his 40th birthday - it is also worthy to note that this is the only time in canon where Ray is not wearing his sunglasses, although as the overdub is audio-only we still never see his face.
The 2004 'Lucky Leo' pilot (Found)
Before the series was picked up by the BBC, a pilot episode called "Lucky Leo" was fully made in 2004 and later recycled into the series 2 premiere episode of the same name in 2007. As Tony Collingwood explains:
"I wrote Lucky Leo as the pilot episode, and we made it at our own expense to pitch the series. ... Lucky Leo went out as episode 27, with some very minor changes. I think we just re-timed the gag at the end when all the meteorites miss the “lucky” Earth. Apart from that – the episode is exactly the same as the pilot. We held the episode back in case we fell behind in production, and could throw that one in to catch up! So we used it half way through to give the crew a breather!"
Update as of Nov 2nd, 2017 - The pilot is finally able to be declared found on an extremely rare 2004 publicity sampler DVD. Far from being "exactly the same", there are numerous differences: just to name a few, the entire SFX track is completely different - using temp stock effects because the foley hadn't been recorded yet - about 70% of all the voice lines are alternate takes, the UZZ Base is an old design with satellite dishes on the sides, and the animations in the Briefing Room are very different too, utilising flickering shadows from the fireplace - an effect which was later dropped completely.
The Sounds Of The Secret Show (Found)
Following the production of "Actors Playing U.Z.Z." and "Artists Drawing U.Z.Z.", a further making-of short known as "The Sounds Of The Secret Show" was made for the ill-fated Volume 3 DVD. Having been previously unheard of, it was uploaded to YouTube with the "Flick The Switch!" commentary and befell exactly the same fate.
As of Nov 22nd, 2017, it has finally been found. It is the longest BTS made for the show, clocking in at 9:27 long, and it chronicles how they made the foley, sound effects, and music used throughout the show. There was previously thought to be a 4th BTS called The Music Of The Secret Show featuring Roger Jackson (the series' composer), but as he appears prominently in the latter half of the 3rd BTS it's existence has now been debunked. It is unknown if there is still a 4th BTS on another topic, however.
A small set 15-second teasers were made for the show's launch in 2006 on CBBC's block known as "TMI". Produced for "Saturday Mornings" (the company not the time), there was one for Anita, one for Professor professor, one for Changed Daily which was recycled with slight editing for the Nicktoons premiere a year later, and.... that was all that was known. It was considered odd that no trailer for Victor had been made, and was presumed "Existence Unconfirmed" for a while - this has finally been confirmed because as of Nov 23rd, 2017, the Victor teaser has been found!
The Last Professor Professor Lectures
Accessible by finding a particular 4-digit code in the background of an episode, these "lectures" were a set each about Professor Professor presenting a slightly chaotic powerpoint presentation on a different topic. Four have been confirmed to exist but only the first two have been found - "Know Your Baddies" and "Inside U.Z.Z.". Very little is known about the last two shorts as they were supposed to be on the Vol3 & 4 DVDs which of course were never released.
The CBBC Platformer
The first truly interactive media made for the show, a 2D platformer game titled "Find The Secret Thing" was available on the long-gone Secrets & Spies section of the CBBC website between roughly 2006 and 2009. Predating the TheSecretShow.com website, it was the first game made by Complete Control for Collingwood/O'Hare. A video showcasing parts of it was uploaded to the developer's Dailymotion and Veoh channels. The game's original filename was "framework.swf" in the "spies" directory on the site.