Encoding an URL in brainfuck
Pyth - 118 bytes, score: 154 + 567 + 597 + 620 + 530 + 875 + 1092 = 6630 6623 4653 4435
Now using the factor multiplication algo!
This is a pretty simple algorithm, although slightly better than the above ones. I was planning to use Pyth, but with the current algorithm Python fits&lt;140 bytes.
=zecz&quot;//&quot;=z?&gt;z4}&quot;www.&quot;zz=z?Pzqez\/zFNzKCNJ/^K.5 1=d\+pk+holN[?*-KZd&gt;KZ*-ZK\-+\&gt;*dK+++++\&gt;*Jd&quot;[&gt;&quot;*Jd&quot;&lt;-]&gt;&quot;*-K*JJd)\.=ZK

It first strips out the http:// by using split(&quot;//&quot;) and the www. and / at the end. Then it uses the min function to check which is the best of the the three options that is considered:

Use + or - to update current cell value to desired cell value
Go to new cell and just fill with +'s
Go to new cell and use multiplication to update by doing sqrt(n)*sqrt(n)+remainder since square has minimum perimeter of constant area. http://cydathria.com/bf/bf_ex3.html

I then always put a . to output each char.
A detailed explanation of the new code is coming soon. I kind of half-assed the golfing, especially the stripping of www. and the / at the end but I can't be bothered since I'm 20 bytes under the limit.
This surprisingly works on the ftp:// urls since this is chrome and chrome automatically makes ftp.freebsd.org/pub/FreeBSD/ into ftp://ftp.freebsd.org/pub/FreeBSD/
I plan to next use a dictionary to store the cell values and see if the character was already made in a cell.

Brainfuck Omnibox Extension
That's right! After I saw @BrainSteel's comment, I knew I had to make it. This doesn't take over the entire omnibox, only when you do bf,tab. Also since the omnibox api is weird, it doesn't let me forward the code to the omnibox, I have to handle it myself. So I do my own http:// checking and then set the tab's url.
Since I didn't feel like paying the $5 necessary to put your extension on the webstore, you guys will have to install it manually. Just download the zip from here: https://drive.google.com/file/d/0B0qkKIzGc0QiNzBzVUJjZkRIZ0k/view?usp=sharing, unzip, go into the extensions page in chrome, click dev mode option box on top-right, and load the unpacked extension.
Hope you guys enjoy! :)