It's pretty well established that the VV story takes place immediately after the first season of Lion Voltron.  But where exactly does it fit in the context of LV's second season, the "Fleet of Doom" special, and V3D?  Following are a couple of my theories.  Personally I don't really lean one way or the other; both theories have their own sets of strengths and weaknesses.  I'm just hoping to get thought processes (not to mention emails) going.  If anyone has other ideas, I'd love to hear them.  For both timelines I started with the LV chronology from Shannon Muir's page and simply inserted the VV series.

Chronology 1:
LV Season 1
VV Season 1
Fleet of Doom
LV Season 2
Voltron 3D

Some reasons for this scenario:
1.  At the beginning of "Fleet of Doom" the narrator says that the Galaxy Alliance was enjoying peace in the Near Universe, thanks to VV.  The most obvious implication here is that the story occurs after VV Season 1 in which the "warlike" Drule faction, led by Zeppo and Throk, had been defeated and sent into exile by VV.

2. Captain Newley doesn't appear in FoD.  This makes sense if FoD occurred after VV Season 1; Newley was reassigned away from the Explorer about halfway through the season.

I suspect that the scenario above is what the original writers had in mind.  But let's face it; the Voltron story has kinda taken on a life of its own in the years since.

And now here's another theoretical version of things...

Chronology 2:
LV Season 1
Fleet of Doom
VV Season 1 and LV Season 2, concurrently
Voltron 3D

Some reasons for this scenario:
1.  In "Help not wanted" (ep 7? ), Hazar expresses his desire to capture the VVF and send them to the slave dungeons of Planet Doom. (Another one of those connections!)  So clearly, Planet Doom was up and running at this point.  (Although it's entirely possible that the Drules, and not Zarkon, were ruling Doom directly at this time--at least until Zarkon could rebuild his forces enough to regain control.)

2.  In "Letters from home" (ep 35), Chip gets worried that something bad happened to Pidge when he doesn't get a letter from him.  It seems unlikely that Chip would be so worried if Planet Doom was still recovering from defeat in LV Season 1; they could hardly give Arus much trouble.  Again, though, that doesn't necessarily mean that Zarkon was the one in charge of Doom at this time.

3.  In "Fleet of Doom", Viceroy Throk leads the Drule attack on planet Acura, not Hazar. The obvious (and, I concede, the writers' likely intended) implication is that Hazar was no longer part of this faction of Drules, having led the coup against Zeppo.  But if FoD happened before VV season 1, it's not unreasonable that Throk might choose to personally oversee such a vital attack and leave Hazar and his subordinates to continue pursuing their given mission.  They WERE in dire need of a new planet, y'know.

4.  Likewise, the Galaxy Alliance commissioned a special ship to transport the VVF to Acura, rather than sending the Explorer herself.  The Explorer was investigating the same space the Drules were, and a complete withdrawal from the region wouldn't have been anymore prudent for the Alliance than it would for the Drules; the Alliance was also in dire need of new worlds.  Also, if FoD happened before VV Season 1 (and hence before Newley was reassigned), then it's completely possible that Newley could have been left in charge of the Explorer and defended by a skeleton crew of escort ships in order to maintain the balance of power in that region.

Side note:  I've had an idea about Cossack's orgins and the Drule occupation of Doom at the end of LV season 1.  He just appeared out of nowhere at the beginning of LV Season 2.  Where the heck did he come from, anyway?  Well, I think he may have originally been a Drule Empire toady from the Drule occupation.  When Zarkon regained power he kicked the Drules out--except for Cossack, who somehow convinced (or more likely begged) Zarkon to let him work for Planet Doom.  I know, I know:  Why in sanity's name would Zarkon keep a doofus like Cossack around?  Maybe to help keep Lotor in line by hanging the threat of replacing him with Cossack over his head.  Also, intelligence doesn't exactly seem to rank very high on Zarkon's list of high-commander qualifications; just look at Yurak.  Zarkon seems to prefer his commanders be ruthless, dumb and obedient.  Maybe he finds some sick amusement in keeping around such "bunglers" who are just competent enough to be useful. :)