Vanguard's trading platform is horrendous, but if it's just for buy & hold with occasional rebalanced, that shouldn't be too big of a deal. Scottrade is pretty good and their stock trades are $7, however they do have a huge list of NTF mutual funds as well. Many of which are very low cost index funds of all sorts. TDameritrade is good too and they have a huge list of free ETF's. I think Schwab and Fidelity have also gotten into the game regarding free ETF trades too. I have accounts with the first 3 I mentioned along with IB and for a retirement account, assuming you don't want to trade futures, etc, I would recommend Scottrade or TDA.
I get the concern and that's definitely on my radar screen as well. That's why I am a fan of account diversification, although it can be a pain in the ass at times. IB looks solid enough for me to have roughly 25% of my trading funds there. They keep fairly conservative on margin requirements which I appreciate. I simply wouldn't feel comfortable with the small shops that offer $500 e-mini margin requirements.