So, I'm on a LC diet, with around 65% fat, 25% protein, 10% carbs. I'm pretty happy with it, but I'm trying to address some of the deficiencies caused by not eating so much fruits/vegetables.
These are the values of vitamins & minerals that my actual diet provide without any of the supplements I'm taking: http://imageshack.us/photo/my-images/37/capturadaaa.jpg/
I feel confortable with a supplement-what-you-don't-get-in-your-diet policy, since that way I don't have to be micromanaging everything I eat. I'm currently taking Vitamin K2, D3, Calcium, Magnesium, and a tablet of minerals every once in a while, since I do want to address the specific needs of my diet, not just take a multivitamins with god-knows-what.  Do you think that is a good policy to have on this matter? Why?
Well, here you have the chart of vitamins & minerals with my diet+supplements, in which you will see I'm low on Vitamins A, Thiamine (B1), and Folate / Folic acid (B9): http://imageshack.us/photo/my-images/713/capturada1y.jpg/
The Sodium deficiency the chart shows does not worry me, since I do not enter the salt I use into Cronometer. About Potassium, that has already been addressed as I just got 595mg Potassium Gluconade, which I plan to take twice a day (that would mean around 4000mg of total potassium a day, which would meet the requirements).  What are your thoughs about this?
Finally, and these are my main doubts:
 Do you think I should also supplement with beta-carotene (or Vit. A?)? If so, in which amounts?
 What are your thoughs on Thiamine (B1), and Folate / Folic acid (B9)? What should I do about that?
 Do you think Vitamin C levels should be highly above the RDA? If so, why, and how much?
Thank you for your help, and your answers!
Here's a post I wrote on n=2 experiment of supplementation with low carb: http://paleohacks.com/questions/111743/what-supplementation-foods-have-you-dramatically-changed-when-shifting-from-highe#axzz1tuXq4vpL
FYI most Paleo people supplement with a magnesium chelate from 200-800mg/day like magnesium citrate, orotate, maleate, gluconate (but oxide is a waste of money and hard to absorb)! You start with 200 mg/day and work your way up in 100-200 mg increments until you get the runs so you know your threshold. Don't try this at the same time as Vitamin C threshold because excess Vitamin C gives the runs too and you need to figure out which one is causing it!
For Vitamin A: I would do the preformed like Green Pastures Fermented Butter Oil.
For Vitamin C: I started with 500 mg/day of Vitamin C supplementation (with Bioflavonoids) and worked up to 4000-6000 mg/day (depending on the day) before I saw GI distress like abdominal pain and/or diarrhea! The hubby went to 6000-8000 mg/day before seeing Vitamin C excess symptoms! We were both seriously too low! US RDA be damned! Keep in mind the 4000-8000 mg is divided into 2-3 doses a day!
You need to test by increasing by 500 to 1000 mg at time to find your threshold!
For B Vitamins you want the Metfolin (folate) not the folic acid. The folic acid can even make your need for folate increase. Folate is the form best absorbed.
I take Douglas Labs B Complex with Metfolin/1 tablet/day
Thiamine (Vitamin B-1, as Thiamine HCI)..... 50 mg 3,333%
Riboflavin.......................................................20 mg 1,176%
(Vitamin B-2, Riboflavin-5-Phosphate)
Niacin ( Vitamin B-3, as Niacinamide)........... 50 mg 250%
Vitamin B-6 (as Pyridoxal-5-Phosphate)....... 20 mg 1,000%
Folate (as L-methylfolate, Metafolin®) ....... 400 mcg 100%
Vitamin B-12 (as methylcobalamin) .......... 500 mcg 8,333%
Biotin .........................................................300 mcg 100%
Pantothenic Acid........................................... 50 mg 500%
(Vitamin B-5, as d-calcium pantothenate) Intrinsic Factor (from porcine) ....................... 20 mg *
Supplemental beta carotene has been shown to be dangerous time and again. Preformed vitamin A is retinol and that, in balance with D3 and K2, is the form most useful for humans.
As for "eating fewer vegetables" on low carb, keep in mind that the soluble fiber from your veggies is metabolized into short chain fatty acids that are quite beneficial for not just colonocytes but for your entire metabolic profile. It can be said that a diet high in vegetable matter is a high fat diet.
Stay away from folic acid when possible. It is a synthetic substance that never existed in nature until a few decades ago. We still don't really know what a human body's response to it fully is. Just go for the real thing, folate.
Your body processes the vitamins in fruits and veggies far better than it does supplements. Why not eat a carrot for beta carotene? If you insist on supplements, your best bet is to make certain they are made from whole foods and not in a laboratory.
I cannot cook fish or seafood in my house (hubby is severely allergic), so I supplement with New Chapter's Whole Mega whole fish oil. My grandmother had her thyroid removed last year and her parathyroids are shot, so she takes calcium daily. Her calcium levels fluctuated wildly on standard drugstore calcium, so I put her on New Chapter's Bone Strength Take Care. Her body really does well on it and she has had no fluctuations in the year she's been on it. (I subscribe to the Bone Strength on Amazon's subscription service and it is cheaper than I've found it anywhere else.)
"About Potassium, that has already been addressed as I just got 595mg Potassium Gluconade"
Don't do this. Potassium in most pills only has 100 mg in it, the rest 500mg are fillers (potassium is not stable as a material to put into pills at higher concentrations). The way to get more potassium is either via potassium salt (I bought a 12 pack "nusalt" from Amazon and I use it occasionally instead of iodine salt), and by eating beet greens (most potassium content than any other food). Fry your meat in a pan, remove the meat, chop them greens, add to the same pan, add garlic, a bit of bone broth, and cook-fry them for a while.
As for the rest of your deficiencies, I show the exact same deficiencies as you do on Cronometer. Which means that either their data are wrong, or on Paleo we do get these deficiencies. Personally, I eat liver once a week for its vitamin A, and I consider fermenting lentils for its manganese/iron/folate/B1 (fermented lentils don't have many lectins left). For now, I supplement heavily though on all of my deficiencies, except for A. For folate, I supplement with actual 200% RDA folate (not folic acid) once a week. 375% RDA Iron once a week. I take manganese as part of a biotin mix once a week, potassium via nusalt once or twice a week, C+bioflavonoids 2-3 times a week, Mg 3-4 times a week, K2 4 times a week, D3 5000 IU almost daily, and some other antioxidant extracts.
Also, I do goat/sheep dairy (butter/cream from cows only), so my Calcium is at around 75% RDA (yours shows to be too low). I personally do not subscribe to the Paleo wisdom that we don't need that much calcium as the RDA suggests, and that we can absorb it better. IMO, we do need calcium from dairy, but from the right animals and only fermented (US cows have incompatible casein, and non-fermented dairy have lactose in it).
BTW, on Cronometer make sure you change the default value of D3 (click on it), because Cronometer uses just 400 IU as its base, which is super-super-super low. So if you're not supplementing with D3, and you're not out in the sun a lot, you're probably deficient of D3 much more than any other of the ones we discussed so far.