Hi Boyd,
For the last couple of years, I've had separate personal and work journals. In fact I had (e.g.) personal-2012, work-2012, and work-clientA-2012, work-clientB-2012 etc.
Having each client in its own file was a specific goal, to make it easier to browse all of a client's history at a glance. Dividing by year reduces the data size and helps with speed (for hledger - ledger maybe doesn't care!). Also, it isolates current data from changes in past history, e.g. "harmless" cleanups. If my balances get out of whack I know I only need to debug one year.
I handled "inter-file" transfers just by putting them in one of the files. Other folks put them in both files, as transfers via an imaginary third account (whose balance will remain zero if you are doing it right).
I had LEDGER_FILE=general-2012.journal, which included all of the above. There's also all.journal, which includes all years.
However, this year I'm back to a single (per-year) journal and loving it. Chasing issues and applying cleanups across multiple files became a pain and not worth it. Fortuitously, ledger-mode recently became able to show a filtered set of entries, which is handy for those client histories (thanks Craig!).
I have a consistent (within each year, at least) set of accounts, independent of the file organization, that cover my personal and business finances. As a sole proprietor in the US, these are fairly closely linked. I learned from my accountant to record my finances from the business' point of view, with my personal expenses under equity:draw:personal. Now, I prefer to write expenses:work:* and expenses:personal:*, which I find more intuitive and easy to enter. If I need to show numbers to my accountant I alias the account names back to her terminology (there's a small example at
http://hledger.org/MANUAL.html#account-aliases ). In general I say use any chart of accounts that makes sense to you now, you can always use account name aliases for reports and experimenting, and global search-replace when you see a better organisation.
So it sounds like you're on the right track. I hope this helps a bit. Welcome to *ledger! I also came from Gnucash. I wonder what's the state of Gnucash these days, why you're considering switching, and if you'll still use it for other things.
-Simon