I have an extremely wierd Kog'Maw build which I've found works quite nice.
I would like commentary on it as well as feedback on the pros and cons of it, with potential other builds.

I start mid with a dagger and a health potion.
From their I build all the parts of the Madreds Bloodraiser before moving onto anything else.
Then I get a pair of sorceror's shoes so that his w and the Madred's deal as much damage as possible.
A Malady for more penetration and atk speed.
Then I get 2 Hextech Gunblades.
Usually around there is where the game ends. But as a 6th item a Phantom Dancer or a Narshor's Tooth comes in.

By the 5th item in this build Kog'Maw with his w running dealing 12% of their hp magic damage with 196 physical damge 1.7 times/ sec (more with the last item) and penetrates for the 12%.

I use 21-9-0 to gain more magic penetration and armor sundering and everything except crit based stats in offensive aka damage, atk speed, cd reduction and magic pen, AP, and so on.
Runes
Red: Magic Penetration
Yellow: Dodge
Blue: 6 Magic resist 3 Magic resist/level
Purple: Magic Penetration
This gives 14 magic penetration, 6.8% dodge, 8.9 magic resist, and 8 magic resist at level 18.
Combined with items and masteries.
Kog'Maw would have 56 magic penetration (after his 4th atk +15%) to ensure that the 12% is dealing its effective amount.

To me this build is made to even the scales between the tanks, and the not. Even heroes with 100 MR won't be too bad as you'll reduce him to 29 MR after the 15% and 56 penetration.
With the 200 pysical damage the more squishy will be takin down even faster.

This build to me makes a lot of sense as it shuts tanks from thinking they're all that.
Only time I had trouble with it was when I had a 250 MR Nasus with 150 Armor. But then we had a suicidal yi on our team he cleaned that up for me. Also, since he had only armor and MR items nasus couldnt deal too much damage. which made him a worthless target anyway.

Anyone want to comment on this build? I've had success working with it and I wanted to share it since I've never seen anyone using a similar build. (other than straight ap which is much different)

I wonder what your attack speed is? Since you seem to want to focus on Bio-Arcane you really want that attack speed cap.

I use a strange Kog'maw build too which is somewhat similar (except your runes are even more wacky than mine, and my masteries are more AP focused). and so far only lost like 2 matches with it.

I feel like you would be better off with mana/5/level runes in yellow and blue (if you use Artillery and such), you really shouldn't need dodge chance and MR because you really shouldn't be getting hit a lot. I pretty much build a glass cannon though, with the occasional banshee's, since his ludicrous range prevents me from taking much damage in team fights.

Sure, Ill bite:

a) I recommend the sorc shoes earlier. This maximizes the effect of your Ultimate and your Puke early on when they are most effective.

b) That is one EXPENSIVE build! Especially 2 gunblades which have Uniques that dont stack of course. By the time you have Malady, Bloodrazor, and sorc shoes the game is many times decided, whereas you have another 8000+ gold worth of stuff you want. You are paying a lot for AP which just doesn't do much...especially endgame.

c) It is kind of unfortunate to stack both Physical damage as well as Magical damage. you have no physical penetration and even the scrubbiest Teemo will have 80 armor to contend with. A Sword of the Divine is probably a better option due to very good AS, magical damage and MINOR ability to penetrate some armor for the physical you DO deliver. Wits End is also a good choice.

d) I like Malady as an option and you might wanna run it first. Once again, its much cheaper than bloodrazor and provides a much needed AS boost, as well as the AP which is helpful to boost Puke early on when it matters more. The extra magic pen is great midgame comboed with your runes and shoes.

e) Why a Dagger? You typically last-hit and snipe where AS just isnt that important. Why not an item that will be more helpful during laning? Maybe boots +3 heal pots? You need boots anyways, so that won't delay your build.

f) You need mana bad. Kog has a great Ult and to use it, you need mana. Otherwise you are wasting his potential. I start with Meki -> Chalice as its 890 gold but adds very helpful magic resistance to help me survive ganks, and unlimited mana pretty much.
When enemy casters can penetrate 30 MR, its nice to have 60 to keep your 23% reduction!

1.7 after the 3rd item and around 2 if I get a second atk speed item.

@ Warrrax

It is an expensive build.
As well as I've noticed my move speed takes a hit. However, by the time I get the first 3 items its usually around 30 minutes into the game, a not decided point.
The Gunblades are for the 75 AP 60 AD and 20% lifesteal 20% spellvamp.
Its to correct Kog'Maws lack of AD and throw people off once they decide they need MR. Around then is also when its a more flexible build.
Also, I misspoke when I said dagger. I meant Long Sword. My mistake.
So you don't think the lifesteal and AD factors as well as the ap which gives another 2% for the bio arcane as well is worth the cash for the 2nd Gunblade?

Sword of the Divine does sound like a nice choice. I'll swap it out next game to try it.

Anything else?

(by the way thank you)

Spellvamp doesn't work with W...

I'd suggest trying out Nashor's as opposed to a second gunblade. It'll give you enough AP and it will give you atk speed/cooldown which I'd say is more important than the stats your getting out of a second gunblade. You could even try two Nashor's instead of 2 gunblades, since thats a bonus 100% attack speed for minimal loss unless you really like the gunblade active or something.

Between Madreds, Phantom Dancer and Nashor's + My Runes I either get 2.3 atk speed or the full 2.5 (I forget). In any case, this gives me 2 slots to beef up my AP and mana or grab something like Frozen mallet for the survivability and the slow. In my build I get the same %health damage that you are (6% + (2%) + Madred's 4%) only I'm capping my attack speed as well, which is more important for your W than additional physical damage, which barely benefits Kog at all save for perhaps taking down the glass cannon builds. I also have a larger mana pool and regen which allows me pretty much unlimited staying power and I am pretty free to spam Artillery and puke.

My build usually looks something like Madred's, Nashor's, Archangel Staff, Phantom Dancer, Sorc Shoes, and for a 6th item either something like Frozen Mallet or Starks, Banshee's, or even a second Nashor's or Archangel if I feel like I don't need the survivability.

My runes aren't finished yet for Kog but they will be mPen Reds, Mana/5/level Yellows/Blues and Atkspd Purples.

QFT. IMO there isn't really a reason to use SO MUCH gold when you dont even benefit very much from Gunblade. Most of Koggy's damage is magic, as you have noted, and doesn't synergize with lifesteal OR spellvamp. So why use so much gold on your (fairly useless) Gunblade(s) when you could use it to get AS capped?

My personal choices for items are:
Core
-Bloodrazor
-Sorcerer's boots
-Nashor's Tooth
-Malady

Situational
-BV
-Glacial Shroud
-Guinsoo's Rageblade (i know it sounds silly, but you keep/get your 8 stacks really easily, which lets you rape all the harder)

I usually go,
Half Mpen Half crit reds
Mp5/lvl yellows
Ap/level blues
Health Quints
9/0/21
Regrowth Pendant -->Philo stone
Zerks
Phage -->Frozen Mallet sometime after madred's depending on the game
Wit's End
Madred's
Hexdrinker/Starks depending on how much magic damage they do

More hp and mana regen while laning and gold/5 so you can finish the build decently solo or duo if someone else needs solo more
Wit's End + Hexdrinker keeps you alive through AP burst and WE counters casters while laning if you get it quick enough
top out around 2 and change for AS
Get Madred's just in time to be useful in time to keep you viable in team fights

Thats going to change my build then. Thank you for that realization. Ive been getting stupid 4th items this whole time then.
Maybe I should go Phatom Dancer, Narshors, or rageblade as my 4th, . I'll play around with it. I really want to base my damage around physical though so I don't think AA would fit my build.
Also I think if its heading this route I'll need a Blood Raiser. for its extra damage and vamp.

Thanks everyone for your help.