The most basic step is making a jig.
Clamp the jig to your drill press table
and you can just put in the blank press it up against the stops and drill down and put the piece on the result pile.
You can also center-punch the holes before drilling.
This will help align the drill bit to where the hole should go.
Put some wood screws through a piece of scrap wood (with a little protruding on the other side) with the same spacing as the holes should be and tap it onto the blanks.
As for the bit I suggest a forstner type drill bit.
woodworking.stackexchange.com/users/20/ratchet freak
Are you set on manufacturing these yourself?
Because really, "best and most efficient" is to get a company with either large industrial machines or low cost labour to manufacturer this part for you.
If you're limited to a standard drill (hand drill, drill press, etc.)
then you're going to get the most efficiency by stacking the parts so that you can drill multiple parts in one pass.
The longer the drill bit and the larger the press, the more you can do at the same time.
Multiple spindle drills, as Daniel suggests, will give you another big bump in efficiency.
You can also scale up with people.
A couple friends and a few cases of beer might go a long way.
You should also factor in that you will likely need to produce more than 5000 as your yield probably won't be 100% -
some will get damaged, holes will be misaligned, etc.
Lets say you can drill 3 boards at a time with a standard drill (one hold), and 3 friends (4 people in total).
You now need to each drill 1,250 holes.
If you can drill 2 holes a minute (I'm just guessing here)
you need 625 minutes or almost 10.5 hours each to complete this.
That is only a day or two of work, just for the holes.
woodworking.stackexchange.com/users/11/Steven
The key to efficiency will not be how many parts you can stack, but rather, how quickly you can set up the next part for drilling.
Set up a fixture with appropriate stops so it only takes a second to pull out the current part and drop the next one in and have it perfectly aligned.
Group your parts into manageable batches (as Jasper suggested in a comment).
Set up the stops to drill one hole on every part in the batch, then set up the stops for drilling the next hole in each part.
You should use a high-quality carbide-tipped Forstner bit for faster drilling, but as always be certain to back the drill out periodically to clear the chips/shavings and reduce heat buildup.
Consider adding a strategically-positioned vacuum to clear shavings as you drill.
A hole saw will be too slow since you'll have to pry out the core after each hole.
A hole saw also wouldn't work very well if you need to make a stopped hole.
You could also use a spade bit, twist bit, or (as Daniel suggested in a comment) an auger bit.
Regardless of which bit you use, it goes without saying that you should use a sacrificial backer board to prevent blowout on the back side.
It's also a good idea to drill from both sides rather than drilling all the way through, but you may find that with the backer board you can drill all the way through just fine.
If you have a powerful enough drill press and a multi-spindle head that's capable of drilling 3 holes at a time, as Daniel suggests, (either all 3 in a single board, or 3 boards lined up next to each other), you can cut your time by about 66%.
woodworking.stackexchange.com/users/49/rob
You can find multiple spindle drill press attachments which may suit your purpose. http://www.hypneumat.com/multi-spindleheads.html
More expensive models are adjustable.
This page has some adjustable models as well. edit
Rather than Forstner bits
I would go with auger or spade bits.
They will handle the deep cut faster.
The trouble is that they have tearout.
To handle that, you can drill partway through then flip the piece over and drill from the other side.
This may be difficult if you don't have your jig perfectly centered.
You can drill until the spur comes through, then align the other side with that hole to finish the bore.
Alternatively, you can use some sacrificial stock under the piece.
This will prevent the wood fibers from moving vertically.
If you're making repetitive bores, you shouldn't need to replace the stock, since the holes will always be in the same place and will still prevent the fibers from moving.
woodworking.stackexchange.com/users/180/Daniel B.
A slightly off-topic approach would be looking into CNC automated equipment, especially if the 5000 units are the first of thousands more.
It is not my area of expertise
but I know small shops use such gear for limited runs.
Once set up, you would still need someone to feed the wood and swap bits, but the drilling would be hands off.
The overhead is the cost of the gear and its set up for task(s), which would include the programming.
There is a hobby-oriented gear as well as full production grade gear.
For a taste of the hobby end, you may wish to visit http://makezine.com/category/workshop/cnc-machining/
woodworking.stackexchange.com/users/111/ewm
I make small hand-craft timber products from my garage and I've recently been approached by a wholesaler, who is looking to purchase large quantities of a very simple product I make.  The product is made of pine and is a 300mm long piece of 2x2 with 3x30mm evenly-spaced holes drilled though the timber.  Anyhow, my question is given I have to make 5000 of these small products, what would be the best/most efficient/productive method of drilling 15,000 30mm holes? And also what drill piece would you recommend?
Best method for drilling thousands of holes?
woodworking.stackexchange.com
<drilling><pine><drill-bits>
woodworking.stackexchange.com/questions/421
woodworking.stackexchange.com/users/200/JasonMortonNZ
S0: The most basic step is making a jig.  You should use a high-quality carbide-tipped Forstner bit for faster drilling, but as always be certain to back the drill out periodically to clear the chips/shavings and reduce heat buildup. A multiple spindle will help. Set up a fixture with appropriate stops so it only takes a second to pull out the current part and drop the next one in and have it perfectly aligned. Group your parts into manageable batches. Really, the "best and most efficient" is to get a company with either large industrial machines or low cost labour to manufacturer this part for you. The most basic step is to make a jig. A  forstner type drill bit is recommended. Consider adding a strategically-positioned vacuum to clear shavings as you drill.  The "best and most efficient" method is to get a company with either large industrial machines or low cost labour to manufacturer this part for you.  Multiple spindle drills will give another big bump in efficiency. You can also scale up with people.  Efficiency can be helped by suitable and manageable stacking of parts and how quickly the next part can be presented for drilling. A slightly different approach would be looking into  CNC  automated equipment.
The most basic step is to make a jig. A  forstner type drill bit is recommended. Consider adding a strategically-positioned vacuum to clear shavings as you drill. The "best and most efficient" method is to get a company with either large industrial machines or low cost labour to manufacturer this part for you.   Multiple spindle drills will give another big bump in efficiency.    You can also scale up with people.   Efficiency can be helped by suitable and manageable stacking of parts and how quickly the next part can be presented for drilling.  A slightly different approach would be looking into  CNC  automated equipment.