This is nowhere near complete, but a bunch of them I remember:
There's at least one shot where you can see a pink thing (Kenny Baker Jr's human face) through the glass "eye" of R2D2's dome. This might have been fixed in one of the special editions, but it's defiantly there in the original. Can't remember precisely where it is, but I think it's one of the "Jawa Sandcrawler" scenes.
If you pause the movie, you can see that the actor in the Greedo costume is replaced by a cheaper looking dummy (with different hands) right before the explosion. This is in the original, mind you, since the scene has been tampered with a lot in the Special Editions.
Obi-wan's lightsaber "fizzles out" at one point during his duel with Vader. In reality the post-production department forgot to color-in a few frames as the saber prop was pointing towards the camera. This was partially fixed in 2004, but I'm pretty sure it's not totally fixed in 2011. There are also a couple of frames from far away where Vader's saber was uncolored (until 2004) and at least one shot which I think is still uncolored in 2004 of the two of them crossing blades, but it might have been fixed in 2011 (not sure, since I don't have that release).
I forget the precise shot (or even what movie, but I think Episode IV), but in some of the external shots of R2D2 in the "socket" of Luke's X-Wing his panels are black (monochrome) instead of blue.
In Ben's Hut when C3PO is supposedly "switched off" you can see Anthony Daniels (the actor in the suit) breathing if you look carefully.
The 2011 edition creates a brand new gaffe by putting a bunch of extra rocks in front of R2D2 when he's "hiding" in that small cave from the sand people. The rocks only appear in closeup, but are suddenly gone again when he leaves the cave.
I believe during the Vader/Obi-Wan saber fight some of the background wobbles.
This is a censorship gaffe. In 1997, Lucas apparently decided that the squib explosions on the chests of the Imperial Officers and commandos that Luke and Han shoot on the death star were too violent, so he censored several of them (deleting frames where you actually see a burst of flame on their clothing from the shot), but he missed one. Watch the scene for yourself and you'll see. Not sure if this has changed a bit since then.
Luke's lightsaber is inconsistent. In the scene on the Falcon it appears as white, while it's blue in the rest of the film. Apparently there were some inconsistencies originally, and the Special Editions have just made it worse and worse. By the latest edition it changes from green to blue and back again several times. It also wobbles off of its handle slightly.
The computer readout "Death Star plans" are clearly flawed, as they show the "dish" along the equatorial trench, whereas in closeups of the Death Star model in space clearly show the dish and the equator are separate.
Several shots of obvious "garbage mattes" (square boxes around space ships that are darker than the space background) appear throughout the film. Some were corrected in the special editions but many remain, though they can be "hidden" if you mess with the contrast/brightness controls on your screen/projector enough. This is true of all three films, though in ROTJ they are mostly green mattes so the brightness/contrast trick won't help you there.
Another 1997 Special Edition gaffe is that all of the added CGI X-Wings we see have the same markings on them (two red stripes on the wings, indicating "Red 2" even when its clearly someone else like Luke, who would be Red 5 and thus should have five red ticks on his wings).
A Special Edition gaffe was introduced in 2004 when the color was sucked out of the Death Star explosion and a blue-screen artifact was added. This was partially corrected in 2011 (the blue effect removed, but the color still nearly monochromatic from how it looked in 1997, and recall that the Death Star explosion in the special editions of ROTJ looks just as colorful as ever).
In the 1997 Special Edition, the scene of Luke and Biggs talking to Red Leader was inserted. Though this was footage from 1977, there was a new "cut" added. To remove a bit of a line about Red Leader meeting Luke's father when he was just a boy, a wipe was created using the passing by of an extra in the foreground. You can see that there was a cut by looking at the "hose" lowering the R2 unit in the upper right corner, as he "jumps" during the cut.
In the 1997 Special Edition a bunch of extra moisture vaporator ("antenna") were added to those that were visible in the 1977 version of the scene where Luke is going to meet Owen with the droid sellers on Tatooine. These CG vaporators are suddenly gone later. I'm sure some fanboy will say that they retracted into the ground or something (but not the other ones), right?
When Vader is talking to Tarkin in the conference room about Leia, Vader finishes his line and yet continues to gesture with his hand, as if still talking. This is because of a difference in the timing of Dave Prowse's original voice acting compared to the dubbing of James Earl Jones.
You might not call this a gaffe or close to it, but since 1997 when the new Jabba footage was inserted, there are a couple of odd things: The dialogue is almost verbatim what we saw just a short time ago in the same movie during Han and Greedo's confrontation.
Jabba looks like he does in Episode I with different coloring, not ROTJ (since 2004 when it was changed from the awful CGI in 1997 that looked nothing like Jabba). He certainly acts out of character but you might be able to explain that away based on the scene as it was originally written (though Jabba was not a slug creature and had no tail to get stepped on). Boba Fett was also added in 1997 (the character didn't exist until 1978) and lacks his familiar "mandalorian" symbol on his shoulder armor.
These aren't true gaffes: The stormtroopers have different voices and different heights throughout the movie, though one should remember that the idea that they were all clones came later. Vader's voice sounds different in ANH than in the others as the modulation effect was done differently (this was altered in 1997 to make it sound the same). Also the TIE Fighter models were originally blue, but because of blue-screen problems they were re-painted gray for ANH. As they use improved techniques like green screen in the later movies, the TIEs are blue for the rest of the series, but in many shots blue filters are used to make them seem even more blue, but not always consistently. Vader's helmet and armor is different in every single movie it appears. The laser bolts in ANH look different than the other films, they're usually solid red lines rather than the thicker bolts with orange/yellow cores as later. The lightsaber blades are also slightly different in every film. In ANH they cast bright glows into the face of the actors but not in ESB or ROTJ (due to the techniques used).
When Han Solo is "weak" after his torture and being supported by the two stormtroopers, you can see his arm knocks one of the helmets loose on the actor and he can barely keep it on his head before the scene ends (making it obvious that this isn't a sealed spacesuit as the EU would lead us to believe).
When C3PO interrupts Han and Leia's kiss on the falcon, some metal bits on his arms (that normally attach to his chest) are swinging loose.
When Leia is close to Han Solo (I think it might be the "being held by you isn't quite enough to get me excited" scene), Harrison Ford mouths Carrie Fisher's line to her before she says it.
I still laugh when I see this one... when Vader says "General Veers" (like he's yelling to him across the hall), and whirls around to find the actor standing DIRECTLY behind him, I guess so he can stay in the shot.
After Vader says "apology accepted, Captain Needa" and passes by the supposedly dead officer, his cape brushes past the actor's face and he blinks.
Vader's helmet (the top piece) wobbles like crazy in the wind during the "I am your Father" scene.
Mark Hamill is quite clearly just holding his arm in his sleeve in several shots both on Cloud City and later on the Falcon.
Mark Hamill hops off of the carbon freeze chamber after Vader and it's clear that he lands on a trampoline to break his fall.
At least one shot of the Executor (Vader's Super Star Destroyer) lacks its usual blue/purple coloration and it looks gray/white like the other smaller ships. I'm not sure if this was a Special Edition added shot or not.
The Snowspeeders when they take off vs. when they are flying are inconsistent. Sometimes they have orange racing stripes on them, other times they are just plain metal.
The scale of the AT-AT walker "foot" that stomps on Luke and Dac's crashed Speeder is different (it should be bigger).
Looking at the backs of the heads of the AT-AT drivers, you can see in some shots they have extra decals on their helmets, other times not.
One AT-AT has an external cockpit that is red, but only in one shot.
Not really gaffes: There are two shots of AT-ST's walking towards Echo base during the battle. It's true we never see what happens to them or how they got there, but neither do we see that for the other vehicles, we don't see how the troops got off of the walkers, etc.
The "Emperor's Slugs." Various parts of the mask or makeup that apparently didn't look good during filming were hastily covered over with some black paint or something on the camera lens or film frames in a really shabby manner. This was "fixed" in the 2011 edition.
Earlier in the movie during the Tatooine scenes you can see something similar was done to R2D2's glass "eye" probably because you could see Kenny Baker Jr's face through it again. It's shoddily plastered over with some dark brown/black paint that wobbles.
There is at least one shot (possibly others) of a Stormtrooper who has his white armor cracked BEFORE he's hit by attacking Ewoks.
A couple of Ewoks (I believe during the "they discover C3PO" scene) are clearly wearing cheap masks that lack the fake eyeballs like Wicket and Chief Chirpa. Yes, I know that some of the Ewoks blink in the 2011 edition, but I don't think this was ever fixed.
As Luke is walking into Jabba's throne room if you listen in the background you can hear Greedo's lines from Episode IV being repeated in the background!
Even though the Special Edition replaced Sy Snootles (the yellowish alien singer) with a CGI creature, the original puppet is still present in the film. As the camera pans around before the dance number you can see her off to the left, and you can tell the difference because she has a flapper style feather on her head (why didn't the CGI version have that, anyway?).
Vader's saber changes all sorts of colors in ROTJ. This was actually present in the theatrical version of the film (or at least the first home video versions), but it has only gotten worse with each new special edition. This is true of the entire Trilogy since 1997 as well.
You can see obvious matte lines and Luke is a blue tint next to the Rancor in the pit under Jabba's throne. This was finally cleaned up and corrected in the 2004 edition.
The 2011 edition creates a brand new gaffe by expanding the size of the door on the front of Jabba's Palace when the droids approach it. It looks impressive, but you can see that the size is back to normal (much smaller) later on, especially when the door opens and you see the doorway from the other side.
Vader's forearm suddenly gets a lot longer after his hand is supposedly "cut off" by Luke. Also the railing that gets severed when Vader's hand is cut off is actually cut before the saber hits it.
Obvious (if you're looking at the lower right corner of the screen instead of focusing on Luke leaping) cardboard cutout of Lando hanging from the small skiff during the Sarlaac battle.
Continuity: How did those ropes suddenly get around Han's legs as he hangs from the skiff in the 1997 special edition?
Han's shirt is different when he's unfrozen from carbonite, vs. the one he had on when he was first frozen at the end of ESB.
When Han pulls Leia back after she's wounded in the bunker, Harrison Ford accidentally grabs Carrie Fisher's breast.
Speaking of breasts (you can stop giggling now), the actress playing the slave girl "Oola" (twi'lek dancer) has one of her breasts flop out of her costume as Jabba is pulling her closer to him. The 1997 edition supposedly digitally erased her nipple, but the 2004 edition has no trace of this. I'm not sure how this got by the censors unless it was just too fast, or they decided that it wasn't "really" nudity because the actress was covered in green paint. The 2004 restoration actually removed natural film grain, making the image sharper than it was in the theater, making her nipples visible even through her costume in 2004. George!