I just got a thought of what could this mysterious name represent. It's a Latin phrase "Vi veri universum vivus vici", meaning "By the power of truth, I, while living, have conquered the universe".
 
You may say that there is a U in there so that cannot be it, but back in those times they didn't have a distinct letter for "u" and for "v", so "u" was written as "v". Even after they started to separate the two, "u" would often be capitalized as "V". So with that in mind, this phrase is now written like this:

"Vi veri veniversum vivus vici"
 
Well, that's my crazy theory, anyway. Thoughts?

These are indie dudes who think of shit on a quick instant. I doubt they'd think of something THAT deep for such a low-budget game.

There are five words there, so five Vs, but if you just count all the Vs you get 6, disregarding the universum V.
 
Or it is to do with the Illuminati.

But what if...they are all actually Ws?

They look like spikes. The game has spikes. I doubt it goes any deeper than that.  
 
Would be nifty if it did, though.

@Cheesebob said:

But what if...they are all actually Ws?

Then it's simply the world wide web

Besides the quick look covered the fact that the V's may represent the first name of each crewmember of the ship, which all start with V, and there are 6 crew members

@ShaggE: That's part of it. The other part is that the crew is made of six people, and each one has a name starting with v: Verdigris, Vermilion, Victoria, Violet, Viridian, and Vitellary.

Because they look like up and down arrows, and you primarily flip upside-down in the game. It is so obvious.

either that or someone likes drawing vaginas in ASCii

@valrog: Cheer up! One of the words has two "V"'s in it.

Edit: Double checking, two of them actually has that, doh!

Doesn't the amount of V's stem from the amount of crew members you save?

@Azteck: Yep. Your name starts with V (Veridian), and you save five other V named crew members. I listed them in my post above.

@Tru3_Blu3 said:

These are indie dudes who think of shit on a quick instant. I doubt they'd think of something THAT deep for such a low-budget game.

Just because a game is low budget doesn't mean that it was easy to make or a throw away project for the developer. Playing VVVVVV, it becomes very clear that quite a bit of thought and work went into that game. Jonathan Blow is an indie developer would you say he puts no thought into his projects?

looks the same upside down? right? isnt that obvious? am i totally wrong?

@valrog: It's the Masons what done it.

There is no conspiracy, each V in the title stands for a crew member that you rescue throughout the game

There is no conspiracy, each V in the title stands for a crew member that you rescue throughout the game

Doesn't the amount of V's stem from the amount of crew members you save?