Both of these are S&P 500 index funds from Vanguard:
VFINX - Vanguard 500 Index Inv
VFIAX - Vanguard 500 Index Admiral
They are essentially the same fund, but VFINX has a $3,000 minimum and 0.17% expense ratio whereas VFIAX is the "Admiral" share class with 0.05% expense ration, but you need $10,000 in your account to qualify.
There are other share classes (Signal and Institutional) that have even lower expense but are typically only held by very large 401(k) plans or institutions (pension funds, endowments, billionaires, etc.). For example, the institutional shares of Vanguard 500 Index (VIIIX) have an expense ratio of only 0.02%. But the minimum to invest is $200,000,000.00. Save your pennies :-0
Many of Vanguard funds have a regular and Admiral share class, and in most cases, the Admiral threshold is $10,000.
As for your allocations, I think you should not look at these as separate accounts but look at all your retirement assets (assuming you consider your IRA and 401(k) as retirement accounts) as a consolidated portfolio.
So, don't focus on JUST what's in your IRA -- focus on what's in your 401(k) + IRA.
Focus on your allocations first, then expenses, unless expenses are horrid, and the difference between the two Vanguard 500 funds is trivial.
In most cases, you'll have a 401(k) plan with some good funds and bad funds with regard to expenses. You might want to choose the best and lowest expense fund in your 401k plan (every plan is different, so it's hard to generalize) and then use your IRA to round out the gaps in your 401k.
Typically, you might have a good 500 Index or, even better, a Total US Stock Market index fund in 401k (like FSTMX), and maybe a decent investment grade intermediate term bond fund, but crappy and expensive international funds.
In that case, load up 401k with US Stock Index fund (total market preferred over 500 despite MMM's frequent endorsements of VFINX), bonds, and then use IRA to hold Vanguard Total International Stock Market index fund (VTIAX) up to your desired international allocation (if in doubt, 30% of stock allocation is good, with other 70% to US stocks).
Finally, your company stock. As long as you can liquidate the shares after holding them for a year, then that might make sense. You probably don't want to have too much of your assets tied up in any single stock.