For the first round, I'm not sure you can always form a general rule on which draft position is best. I think it mostly depends on the top players who are available in a given year.
For example, in my mind, there are two top tiers within the first round, and I'd basically be equally happy to have any guy within the same tier:
1. Pujols, Vlad, Beltran
2. Tejada, A-Rod, Manny, Johnson
After this, I think it becomes less clear. Abreu could easily be worth a high pick, but what if he gives you 20-20 (like '03) instead of 30-40? I think that at this point in his career, Helton should be expected to hit 35 HR, not 40 or 45, and I think he'll be hard-pressed to produce many runs or RBI's with the lineup around him. I'm not sure Santana is necessarily guaranteed to have a significantly better season than someone like Schmidt or Sheets, who can both be taken later. I would hesitate to take Crawford in the first round as well. I'd probably be willing to take Bonds, but the risks involved with him are enormous.
So basically, I think I'd much prefer a top-7 pick to any later-round pick, simply because I think that this year, there's a significant drop-off after the top 7. Although an earlier first-round pick means a later second-round pick, I think that the drop-off is more significant within the first round. For instance, even if you miss out on Sheff in the early 2nd, you can still grab Miguel Cabrera in the late 2nd. If you miss out on a first baseman like Teixeira, you can always grab Ortiz. Miss out on Schmidt? Grab Sheets.
Basically, I don't have a general rule for which draft position I want. Based on my tiers, I think that 3rd and 7th overall are the best spots, but I'd be happy with any top-7 pick. I just think that the dropoff after the 7th pick is more significant than having a worse second-round pick or not being able to pick twice in a row. I understand that it's not exactly groundbreaking, but my feeling is basically that the particular players available are more important than any general rule about draft position.