Here's the short version: forget it.
And now for the slightly longer account:
I've many times seen, in various articles, publications, websites, etc., the idea put forth that the various stories featuring Captain Harlock and assorted attendant characters don't fit into any proper chronology that could make any sense at all. After this declaration, which is significant and utterly true, the writer will then proceed to elaborate on some form of overarching continuity, as if they had suddenly been struck with a flat iron and were unable to remember their own prior assertion. Failure dogs their heels throughout the ill-fated attempt, and finally catches them and eats them. They have blown it.
There shall be no schizophrenic doubling back here. I'm here to tell you that any excercise in trying to fit all the Harlock stories under one umbrella is rather like trying to fit all the penguins in Antarctica under one umbrella, which is to say 1. futile, and 2. pointless.
There's a baker's dozen good reasons why it can't work, but let's begin with one of the biggest: a little guy named Tochiro Oyama, Harlock's bestest pal and the creator of the Arcadia, who (to date) has died three times in the animated incarnations of Harlock, in three different ways:
The mere fact of a single character dying more than one time is enough to raise serious eyebrows for most of us, but it might be different if it were the same scene each time, occurring at a convergent place in the continuities of the three storylines. However, it's not. The first time, in the 1978 Space Pirate Captain Harlock series, Tochiro dies from an anemic attack mere minutes after the launching of the Arcadia. The second time sees Tochiro die in the wreck of Harlock's old ship the Deathshadow after catching a "space disease" while in pursuit of the villainous Count Mecha, whereupon Galaxy Express 999's Tetsuro Hoshino assists him in transferring his consciousness into the central computer of the Arcadia, which has been cruising about without him for some time. And then, in the 1982 Endless Road SSX series, he dies yet again, this time catching a space disease after traveling through a wormhole to rescue Emeraldas. He has at this point been traveling aboard the Arcadia for several years, after which he returns to the Deathshadow's wreck to perform the upload of his brain again, only this time without Tetsuro's presence. His skinny-necked pet Mr. Bird is also absent, though he was living with Tochiro in the 999 version of the scene. In SSX, Bird is still on the Arcadia. And while we're on the subject, which Arcadia are we talking about, anyway?
In the Space Pirate series, Harlock is captain of the blue Arcadia, which we see Tochiro build on planet Heavy Meldar, a planet which then, much like Tochiro, buys the farm minutes later. (This planet is seen alive and well in both 999 films and the SSX series, well after the Arcadia's creation.) In the theatrical feature My Youth in Arcadia, Tochiro builds the ship yet again, this time the green, skull-nosed one that has appeared in virtually every other Harlock story since. Moreover, he builds it on earth this time. Are these two different ships?
There have been plenty of theories put forth, often presented as facts, irritatingly enough, saying that one or the other ship was damaged or destroyed, and Tochiro had to build a new one, or rebuild the old one. The fact that there isn't a single frame of animation depicting this, nor do any of the characters ever say anything along these lines, tends to suggest that people are simply concocting comfortable notions to avoid having to deal with the (admittedly mild) brain-bender that both these ships are the same Arcadia. The change in design was due to nothing more than simple marketing issues: Takara owned the rights to model kits from Space Pirate, and Bandai owned the model rights to Galaxy Express 999. When the Arcadia was slated to appear in the first 999 film while Space Pirate was still on the air, it would've amounted to free advertising for Takara; therefore Bandai had Studio Nue design an alternate version for them, to avoid giving their primary competition any leg up. (Studio Nue had also designed the blue Arcadia, and would shortly gain fame for its Macross design work.) In its own way, it's not far removed from having two different actors portray the same character in two different TV seasons or movies, in which cases viewers rarely have to contrive wild notions of secret plastic surgery in order to deal with it. So deal, jackass.
The blue Arcadia also made a cameo appearance in the 999 television series in a three-part episode (episodes 79-81) titled "Pirate of the Time Castle," and has recently resurfaced in the new Queen Emeraldas OVA series (though now painted black.) Of course, its most recent and simultaneously most bizarre appearance is in the new Cosmo Warrior Zero mini-series, where it appears sporting the paint job of the green Arcadia, and is renamed the Deathshadow. Far from reconciling any of the disparate continuites, it simply gives us one more iteration in the category of "things named Deathshadow." The ship Deathshadow, Harlock's first command, appears in both 999 movies, the Arcadia movie and the SSX series, wherein it looks absolutely nothing like the blue Arcadia; in Space Pirate, Harlock's ship is quite definitely known as the Arcadia, while the name Deathshadow is given to a mobile dock for the ship and the actual planetoid it's modeled in semblance of. Continuity, I laugh at thee. Shall I compare thee to a mangled train wreck?
The third in the trio of space pirates at the core of this mythos, Emeraldas, presents her own contributions to this irreconcilable mishmash, the least of which being that in the Space Pirate series, she's known as "Emeralda" instead (though interestingly, in the Space Pirate manga from which this series was rather loosely adapted, she's still known as Emeraldas.) It's also the only version of the story in which she and Tochiro conceive a child, the blue-haired woodwind extraordinaire Mayu. (Or rather, it's the only version wherein this fact is dealt with at all: the Endless Odyssey mini-series actually does show Mayu again, albeit briefly, but never bothers to tell the audience who she is. Newcomers beware.) In pretty much every other storyline, the two are in love but living separate lives, and in SSX, she's only begun to return his affections when he tragically bites the big one. She also may or may not have a scar on her face, a la Harlock. We'll see her get it twice, in two different ways.
There's a baker's zillion of fan articles out there calling the female pirate "Esmerelda," presumably written by people who have never heard her name spoken in any of the Japanese films in which she's featured. Take heed: she is never known by this name in any original Harlock anime or manga; I can only assume that either they've all watched the French-dubbed version Albator, where her name was in fact changed to "Esmerelda," or that's it's just a case of people not paying very close attention.
Newer Matsumoto anime has put forth the idea that Emeraldas and Galaxy Express 999's Maeter are actually sisters who grew up together on the planet LaMetalle (featured in the Queen Millennia series and movie,) but this is plainly a new idea that is flat-out incompatible with the older stories; witness the pair's first meeting-which is quite obviously their very first meeting-in the 1980 TV special Eternal Voyager Emeraldas, wherein the two know each other only by reputation. Any way you slice it-and as you can see, it's already been sliced a good number of ways-there's just no way you're going to get a unified picture from this collection of stories. It's like assembling a single jigsaw puzzle of say, Richard Nixon, from five different puzzle sets; no matter how you piece it together, you're going to get a crook, but one that will look like he was painted by Picasso on a bad day with a live weasel as a brush. It will hurt your brain, and your hand as the weasel attempts impatiently to consume it. Save your sanity and don't try this at home, kiddies.
Let me also point out that the Japanese have no particular standards for romanizing non-Japanese words, so Harlock is occasionally spelled "Herlock" in various places. This is the same character as Harlock, not a relative, clone, or evil robot double. And yes, real flesh-and-blood humans have actually asked that question. I have used the spelling "Harlock" throughout on account of the fact that the Japanese use the pronunciation "Harlock" throughout, as has every English dubbed or subtitled property prior to Endless Odyssey (with the small exception of Roger Corman's Captain Warlock from New World Pictures' dub of Galaxy Express 999, which can be safely ignored.) This could be due to the fact that "Harlock" is an actual name, and "Herlock" is not.
What follows is a list of the various Harlock continuities: what fits with what else and what absolutely does not cross over. Please note that as newer Matsumoto anime featuring Harlock is still being produced, this list may not be 100% complete at the time you may be happening to read it, a fact which remains, as always, entirely your own problem.
Space Pirate Captain Harlock
Galaxy Express 999
My Youth in Arcadia/Endless Road SSX
Harlock Saga: Der Ring Des Nibelungen
The Endless Odyssey: Outside Legend