A mass fabricator can be used to create the versatile uu-matter, but is a complex and resource-intensive process.
Here's a way to make it simpler.
Note that the following tutorial makes the following assumptions:
-You are powering your fabricator using a nuclear reactor. I'm using Rick's cheap MK 1 design on the 'useful reactor designs' sticky in the nuclear engineering forum as a baseline; it's a very useful design.
-You are using buildcraft -- the most efficient cobble -> scrap recipe was created by buildcraft, and the mod has a bunch of useful tools for automating scrap production.
-Overclockers are not being used; I might edit this post later if I learn the formula dictating how overclockers affect energy usage.
-The decimal point is represented by a period, not a comma -- just in case.
-Finally, You are comfortable with math.
Let's begin.
According to the wiki, making a single UU matter at the lowest possible efficiency uses 1 Million EU. Luckily, there is a much better way to create matter: scrap. Adding scrap to a mass fabricator will make it work six times faster, and reduce energy usage likewise. A scrap-powered mass fab will only use up 166,666 EU per matter, but producing matter at this pace requires 34 scrap. Scrap can be produced at a recycler, but on average, it takes 8 recycler operations (35 EU without an overclocker) to produce a single scrap. I takes an additional (34•8•35) 9520 EU to produce matter at optimal efficiency, for a total of 176,186 EU/matter, and creating a single matter consumes (34•8 ) 272 blocks/items. That's a lot of stuff.
The best material for recycler food is cobblestone -- it's widely available, quick to mine, and using lava, infinitely renewable. Again, however, 272 blocks of cobble are required to make even a single piece of uu matter -- but luckily, there is a way to multiply the number of recycler operations you get from a piece of cobble by 8/3 -- 3 cobble can be crafted into 8 buildcraft cobble pipes, meaning that only (272•3÷8 ) 102 blocks of cobble are necessary to create uu-matter, less than two stacks.
But, you say, does the pipe recipe not require glass? That it does, but luckily there is a way to create glass from cobble. Cobble can be macerated into sand at a cost of 625 EU, and smelted in an induction furnace at the cost of an additional 208 EU (For simplicity's sake, I'm assuming that you have a solar panel wired up to the induction furnace to keep it at maximum temperature). One glass is used to create 8 pipes; as a result, using this method to create 34 scrap consumes an additional (34•[625+208]÷8 ) 3,540 EU, for a total of 179,726 EU per UU matter.
As a result, 1 UU matter can be created from 179,726 EU and 102 cobblestone by:
1. Macerating 34 cobble into glass, then smelting it (in an induction furnace) into 34 glass (costs 3,540 EU total)
2. Using your cobble and glass to craft 272 buildcraft cobble pipes
3. Feeding those pipes into a recycler to produce 34 scrap (Costs 9,520 EU total)
4. Feeding 166,666 EU and 34 scrap into a mass fabricator to produce a single UU matter.
For ideal sorting of cobble so that 1/3 of the cobble becomes glass, use a diamond pipe with two cobble in one output slot feeding an automatic crafting table, and 1 cobble in a different output slot feeding a macerator -> furnace -> original crafting table.
Using a 40 EU/t reactor, and powering everything except the mass fab using renewable energy/(geo)generators, a total of (4 million ÷ 166,666) 24 UU matter can be created from (102 • 24) 2,448 cobble (38 stacks plus 16, about 2/3 the capacity of a double chest)
Note: Using diamond pipes, cobble can be easily sorted to make exactly 1/3 of it go to the macerators -- either route cobble out of three inputs, only one of which leads to maceration, or route cobble out of two inputs, one of which has twice as much stacks of cobble as the other -- cobble will be twice as likely to go down that route.
+ 3 
+ 4 manned 
= exactly 5000 EU/t