Whoa man, the EU and the movies are FILLED with contradictions (no offense). That's why there are things called "retcons." That's comic-book speak for something that's been written to explain away a contradiction or change the story to say it was "always this way" but you read the new source to explain the old one, since it doesn't make sense otherwise.
Here's an exercise for you:
Watch Episodes I, II, and III. Then watch IV, V and VI (doesn't matter if you watch the Special Editions, original versions or 2004 editions). You'll note many contradictions, revealed by the following questions:
1) How old is the Republic?
2) Are Stormtroopers all clones of Jango Fett?
3) Who was Obi-Wan Kenobi's Master?
4) Did Obi-Wan Kenobi know of that Leia was Luke's sister?
Notice I'm not talking about contradictions introduced and then explained in the prequels, only contradictions that result after all the movies are taken into account.
Also, as this relates to the EU, after watching the movies, pick up Timothy Zahn's "Thrawn Trilogy" (Heir to the Empire, Dark Force Rising, The Last Command) and read it. Now see the contradictions with the movies based on these questions:
1) How are clones created?
2) Does the Empire clone its soldiers?
3) Did Anakin bring balance to the Force?
4) How many Sith are there?
5) Were the Jedi wiped out? (other than the 3 in the movies, including Vader, and "the other" and Luke after those three died)
6) How long did the Empire last?
7) Do we see any of these EU characters in the movies?
8) Who designed and built the first Death Star? How long did it take?
9) Has the galaxy been explored? Has anyone travelled outside the Star Wars galaxy?
10) Are holocrons mentioned or seen in the movies?
11) How effective is General Grievous against a Jedi Knight or Master in combat?
12) How effective are Jedi Knights in battle against armies of droid troopers?
13) Do Jedi wear armor or space suits? (I'm not counting Luke wearing a helmet in the classic trilogy)
14) Were Wookiees enslaved (as a species or as a world), and if so, by whom?
15) Did the Sith ever rule the galaxy? (before Palpatine's rise to power, I mean)
16) How long after their deaths can Jedi spirits communicate with the living?
17) Do clones "give off a weird vibe in the Force" allowing them to be instantly detected by a Jedi?
You can do the same with the "Dark Empire" and "Dark Empire 2" graphic novels and lots of other sources written before 2005. I'm not saying explanations aren't possible, but there are plenty of contradictions, and that's why retcons are being written all the time. Lucas felt free to contradict the EU and his own movies in making the prequels and the Special Edition changes, creating confusion in the EU and necessitating retcons.
Other questions from these and from a variety of EU sources:
1) How did Palpatine come to look old and wizened?
2) How did Palpatine obtain power?
3) What is Boba Fett's origin?
4) How old is C-3PO?
5) How old is Greedo?
6) What planet are those three eyed aliens (Ree Yees) at Jabba's Palace from?
7) What color are lightsabers used by the Jedi Order? What color are the lightsabers of the Sith?
8) Does Yoda use a lightsaber or not? And did he always "talk backwards"?
9) What caused the clone wars, what factions fought, and how did it end up? How long did the conflict last?
10) How did the Jedi Purge happen, when did it happen, and who survived it?
11) Did Jabba the Hutt (or any Hutts) have any role whatsoever in the Clone Wars and/or Jedi Purge?
12) Did Jabba the Hutt meet with Han Solo in Docking Bay 94 before the Falcon took off for the Alderaan system or was it someone else? Was Boba Fett present?
13) How many members were in the Max Rebo Band at Jabba's Palace? How many dancers were there?
14) When the Emperor speaks to Vader via hologram when he has learned of a great disturbance in the Force, was it a private conversation, or was someone else listening in?
15) How many of Vader's limbs are cybernetic? How and when did he lose them?
16) Is Yoda a unique creature, or are there other of his species?
17) Are Jawas unique to Tatooine?
18) Is Force Lightning a common ability among Force users?
19) Are Jedi allowed to use the force to attack or counter-attack their opponents in battle? (this will be controversial, but just watch the movies then tell me!)
20) Is it possible to use force powers in the midst of a lightsaber duel?
21) Can lightsabers "cut through anything" or do some things stop them? (besides another lightsaber of course)
22) Is the Millennium Falcon too small to have a cloaking device?
23) Do lightsabers work when wet?
24) What was R2D2's origin?
25) Where were the Jedi headquartered? Did this headquarters survive the Jedi Purge?
26) What role did "Mandalorians" and "Clone Masters" play in the Clone Wars?
27) Who was Luke & Leia's mother?
28) How did Anakin "get into the suit"?
29) Were the Death Stars "brand new technology" when they were built, or just a much larger and new application of existing technology?
Personally I think they should just restart the EU continuity with the new completed saga (six movies as they appear on DVD) in mind. It seems to have worked for some comic book franchises, why not the Star Wars EU?
Now before you jump up and explain all of these to me, realize that you're using material outside to explain away contradictions. That's fine. Is it the job of the EU to explain away contradictions? Or is it to "expand" the story beyond what's told in the movies? I'm just saying that if there were no contradictions, you wouldn't need to write new stories to explain them away. Right?
Now here's some of the inter-movie possible contradictions (some could be explained as characters simply lying or being idiots):
1) When did Obi-Wan Kenobi serve Bail Organa during the clone wars?
2) When did Anakin say he wanted his son to have his lightsaber when he was old enough? And when did Owen Lars forbid this action?
3) When did we see Anakin demonstrate being "the greatest starpilot in the galaxy" and "a cunning warrior" and "a good friend." Granted, this is subjective.
4) Was Admiral Motti (the guy Vader chokes in ANH) around when the Jedi Knights served in the Republic?
5) Is the Dark Side stronger? (granted, this may be based on comments by Lucas that create the contradiction, not so much the movies themselves)
6) (not contradiction so much as oddity) Why do Owen, Beru, Obi-Wan and Anakin look so old in the Classic Trilogy? Why are Obi-Wan and Vader such relatively sluggish saber fighters in the classic trilogy against each other?
7) How is Luke's green lightsaber "much like [Anakin's]"? (Palpatine's line in ROTJ)
8) Was Nute Gunray betrayed by Darth Sideous 10 years before AOTC? And if so, why does he blindly trust him again in ROTS?
9) Did Vader really "help the Empire hunt down and destroy the Jedi Knights"?
Now for some major ones within the EU that have problems with other EU sources:
1) How big is the "Grand Army of the Republic" and what does it consist of?
2) How big is the CIS's (Seperatist's) droid army?
3) How do lightsabers work? How does a Jedi Lightsaber differ from a Sith Lightsaber (if at all)?
4) How was Yoda able to hide on Dagobah? What was the origin of the "domain of evil" (the cave where Luke "sees Vader")... when and how did it originate?
5) What is the origin of the Sith?
6) Is the Jedi Order as old or older than the Old Republic?
7) How many Sith Lords achieved the power to cheat death? Who were they?
There's probably many more contradictions one can find. Apart from the official outside-of-movie answers from Lucas or Leeland Chee (which I respect), you can find them on several sites, which I could point you to, including the http://www.soulofthejedi.net
fanfiction archive and http://www.chefelf.com/starwars/