Heres some random thoughts to get this started:
1) Holding individual treasury bonds, individual treasury bills, and physical gold bullion is more secure than ETFs because you remove at least one layer of the counter party risk by holding directly.
2) Having assets at multiple institutions hedges you against temporary or permanent loss at that institution by splitting things up. So if your Vanguard account gets frozen or hacked, its only a portion of your overall assets. On the flip size, if you split your assets into 100 institutions with 1% in each, the headache of maintenance makes this cost prohibitive. How do you find the best balance?
3) Having more than $250k in a Solo 401k in the US is a risky proposition. Once assets reach that point, you must file an annual report to the IRS. One can only assume this is to facilitate confiscation of IRA assets exceeding $250k when things in the US become like Greece.
4) Having too much money in IRAs/401k can be risky overall as CraigR points out because of the general looming threat of wealth confiscation by government. One can easily see a "solution" to government shortfalls is to mandate all IRA assets above $X be turned into the government in exchange for a guaranteed government-backed retirement bond.
5) Gold bullion is the most complicated of all assets IMHO. You want physical but there's really no great place to put it. Chase Bank recently banned gold bullion (and cash) from safe deposit boxes and other banks will likely follow suit. Greece has frozen SDB access and will likely seize any gold in them. Having gold at home risks theft. You can get a safe, but even if you spend $1,000+ on a really good safe like for guns, it needs to be bolted into concrete to be secure. That basically rules out the ability for a renter and possibly condo-owner from securely storing gold at home. You can secure it at a specialized vault but there's counterparty risk. I think I'd rather have an ETF than a "vault service." The state of Texas recently voted (last month) to started their own depository for gold. I'm looking for a place to buy a home and settle down and if I choose Texas, this may be an option for at least some portion of the gold.
6) Equities would be best held as individual equities instead of ETFs due to counterparty risk and annual expense ratios. However, unless you have significant assets ($50MM+), you can't really buy enough individual stocks to match a good ETF and get good diversification. What I'm considering is getting one of the brokerages that offer 50 or 100 free trades each year, and selecting about 30 large cap stocks and buying equal amounts of each. That would be half of my PP equities. The other half would be an ETF. As long as the 30 stocks are in different industries, you'll get really good diversification and if you set dividends to reinvest, won't have any annual expenses. Biggest problem? Getting 30 different sets of voting and annual/quarterly shareholder reports in the mail. I only hold a few individual stocks and getting that crap in the mail really bothers me. I think I've gotten a dozen things from GTU in the last few months alone from the takeover issue. Second biggest problem is while your 30 stocks will be close to the index, it won't match it. So you'll be 1/2 percent up or down and then think you're a genius and decide to gamble away in the VP or you'll be down 1/2 percent and second guess yourself and sell all 30 and switch back to an ETF and have all sorts of transaction costs involved. Probably best to just hold ETFs for all of the equity portion, and possibly split across 2 or 3 different ones. Like Fidelity, Vanguard and Schwab.
7) Having stocks in a taxable account seems great from a tax perspective but also one of liquidity. If the government starts getting to the point of desperation, its easier to get the money out of your taxable brokerage than it is get it from your IRA/401k. CraigR discusses this on the forums.
