Some glitches obviously are exploited by some users, they were never made to be found. But what about Mew? He was [if im correct] meant to be eventually found by us right? What else throughout the years has been hidden MEANT for us to find?
I read somewhere that mew was just a test pokemon that they forgot to take out of the game,and when loads of people hacked the game and found it, GF couldn't just get rid of it ,so it's still in the games.{P}
The only glitch besides the cloning glitch in Emerald and D/P/Pt is the Missingo cheat in R/B/Y. Now, they make sure all glitches are paved over in the English version so no one can easily exploit the rewards from the cheat.
I do not think any cheat was meant to be intentionally found (save for potentially the invisible floor glitch in Japanese D/P games). I believe they are always oversights in the game code, which we gamers like to exploit because it's fun to do so.
All I know of are:
Missingno (this is also used to clone items (I'd go for the Master Ball & Rare Candy's...sometimes even TM's)
Mew-Truck cheat (I've done this one....but I didn't get my Mew )
Cloneing (G/S/Emerald)
I'm guessing that, although they tried to remove the data for these MissingNo.s, they couldn't completely get rid of it because it was already there in the first place (Like dummied out items such as the Red Chain/Magma Stone in DPPt, or the Slowpoke Tail in HGSS; maybe even the Minus World from Super Mario Bros. 1). GSC were programmed to load the equivalent Pokémon in a RB trade involving MissingNo. to keep continuity. I'd suggest reading the whole thread I linked to for some more info.
Also, Mew was intentional, but the glitch involving it was just an awesome programming error. The few people working at GameFreak at the time realized there was just enough extra code to place in another Pokémon after probably removing most of the data from the nerfed 39 Pokémon above (That is probably why they decided to get rid of those guys). However, the actual Mew glitch DNA linked to, as well as other stuff, such as MissingNo. and 'M side effects,glitch Pokémon,the Q glitch,Glitch City,the Celebi egg glitch,Acid Rain,Tweaking,the Freefall glitch, and of course, cloning, are unintended.
Also, Mew being related to the S.S.Anne truck is entirely false. GameFreak does poke fun at this in FRLG, when if you go down a section of the dock that the truck is on, you can find a hidden Lava Cookie, but that is about it.
The Mew glitch was meant to be. The Pokemon Primaries (R/B/G/Y) probably wouldn't have been this famous w/out it. Mew was almost impossible expect for those small events.