I accepted a quest which brought me to a crypt full of mean skellies and i knew i would
need some Greater Soul gems for some enemies because their souls were "great".

So i blew about 3k gold on some empty greater ones, headed to the crypt and started
killing everything... suddenly i get the message "That soul is too large for you to absorb",
i was like wtf... i haven't killed many "greater" enemies yet.

So i brought up the menu and discovered that ALL my soul gems, lesser, common and
greater, was occupied by a lesser soul and all the Greater souls could no longer fit...


Why can a lesser soul inhabit the gem made for a greater soul?. Is there a way to transfer
a soul from gem to gem?. Because currently i have about 40 or so, lesser gems filled, with
no use what so ever. And every time i need to refill a weapon, it uses a common instead
of a bunch of lesser.

/Edit:
I just read on wiki that if you kill a lesser being for its soul and only have a greater or grand
gem available, it will ruin that gem by taking place in it. So that kinda svcks MAJORLY.

From now on i will have to watch what i soul-drain and which gems i have that are empty...
(Kinda makes my Great sword enchanted with Souldrain somewhat useless, unless i save
it for a boss fight).

Sorry buddy.

Smaller souls can go in larger gems.

Like 200ml of liquid can fin in a pit glass.

But 500ml can't fit in a shot glass.

And you can't transfer them

You can't transfer them. Soul gems hold the level they are and below. If you run out of lesser soul gems when you trap a lesser soul it will go into a Common first, then great, then grand. Basically don't soul trap every little thing unless you have a lot of lesser and petty soul gems so your big ones don't get wasted.

A soul will go into the smallest container it can go into.
If you do not have empty lesser gems, it will go into a common, a greater or a grand.

Take enough empty soulgems with you, or only soultrap those you want the soul from.

Buying a ton of petty and lesser soul gems, then soul trapping everything you see is a great way to raise the conjuration skill, the enchant skill, and your gold.

A good ruler to give you an idea of what has what soul...
Wolf=petty
Ice wolf= lesser
Bear= common
Giant= greater
Mammoth= grand

Humen= grand

But can only fit in black gems

That's why Azura's Star rocks.

Blak Star kicks much more ass

Yea, this is an annoying part of soul trapping, i have to constantly check my inventory to make sure i don't have a darned mudcrab's soul in my grand soul gem -.-

This. I thought it would require me to buy SGs to stay ahead of consumption too, but not really I have found. I get plenty from hitting lots of crawls as I travel the countryside. I do have the Azura's Star for the big ones that I use for my enchanting. So don't pour a ton of coin into buying SGs. Can get spendy fast, and a couple of free common or lesser SGs will fill up an item as easily as 1 grand, so save the coin for other needs...

You can't transfer souls but you can empty them.

Drop the filled soul gem you want emptied on the ground, then pick it back up and it will be empty. This might be a bug but it's quite useful.

Next time be careful where you cast soul trap.

Drop the filled soul gem and when you pick it back it will be empty again. So at least you don't waste the money spent to buy it. Of course you can refill it once emptied.
I have the same problem. There are not enough petty and lesser soul gems on sale and the souls of any rabbit or wolf end cluttering the grand soul gems.

Easiest way to avoid that is not casting Soul trap or wasting your soul trap enchant on those types of animals ! (keep a secondary unenchanted weapon on hand for the lesser kills)

Or only take your grands with you when your hunting big game for enchanting.

My character is not a spellcaster. So the weapon is enchanted with soultrap. It doesn't bother me, I just drop the unwanted soulgems from time to time. Once evey piece of equipment is enchanted there is no need for soulgems. Enchaning wih a grand soulgem makes the items too expensive for merchants.

This has been standard for quite a few Elder Scrolls games... so most of us just accept it, and be careful not to use Soul Trap on a Lesser Soul when the only gem we have is Greater.
That said, there are a few troublesome points this time around:

#1. The weighting of the souls in Skyrim is much worse this time around than it was in previous incarnations. Pretty much the ONLY things that you can kill to get Grand Souls are Mammoths (Black Gems aside, since they're not as easy to come by as they were in Oblivion)... There are also Dragon Priests, but they're stupidly rare by comparison. Aside from that, only named super-monsters have Grand souls, and there aren't too many of those. Can't even take the souls of Dragons into gems because your body steals them all.
(p.s. If you're wondering at the best source of Greater souls, as if you need anything less than Grand, the answer is twofold: Giants... and Draugr Deathlords. Both are common enough at higher levels)

#2. Y'know that perk that makes Bound Weapons automatically Soul-Trap what they kill? You know what you're getting into when you select it, but if you decided to select it so you'd have an easy way of soul-trapping enemies, and you happen to use them for everything else too (because dual Bound Swords are surprisingly devastating weapons for a spellcaster)... I know that feeling. The only answer I had was to carry as many lower-level Soul Gems around with me as I could.... or just summon Atronachs to deal with lesser enemies.

#3. Do as we've always done in Elder Scrolls games: Make a main weapon, and a soul-trap weapon. Two of them. Separate. Even on the 360 I have two quickslots to switch between weapons if need be, AND the whole favourites menu otherwise. Point is... only pull out your soul-trap weapon when you need to trap a soul. ;

Yes this micro management can be a bit annoying.

If any future mod reads this, could you make it so that you can toggle whether you want smaller souls to enter larger soul gems or not.