With the new multiple sign in, I use my gmail account as primary, then sign into my other two gApps accounts (personal, work). That way, all my analytics, web history, and such remain under my [primary] gmail account and I can still open multiple Gmails with different accounts in them.

I've found a little lag in gmail to apps features, but not long enough that I've worried about it.

Apps accounts don't play well with a lot of google services. It's quite complicated to grant Google Analytics access to an Apps account.

You don't have to use your apps account only, you can still use your regular one for buying Android apps etc.

Here is the scenario: you have google apps account that you use for all your stuff and you sync it with your android device to access email, contacts and such. This is account A. Then you realize the market won't work, so you sync the regular google account, account B.

Now, you have the hassle of having to deal with multiple account on your phone, but is not too bad. It comes bad when you discover that if reset your phone and sign in only with account A or only with account B or even in the wrong order (B, A), all the apps you bought are simply gone.

Yes, the market sucks that much.