I'll echo that about not even having bonds anymore, mostly because the yield just isn't there.
But if you were, I would put them in something like a taxable. Save your tax advantaged accounts for equities.
As far as fund choice, I prefer total market. Index funds that mirror the SP 500 are okay (SPY), but you kind of miss out on all the small cap stuff. Which frequently has incredible growth. From a finance perspective, it essentially eliminates everything but market risk from your portfolio. Theoretically the formula says you can do that with a mix of 10-15 different stocks, but more is better! It also, in my opinion, eliminates any need to diversify into international. I do miss out on the Nestle's and Sony's and whatnot, but US companies provide enough international exposure for me.