Well, I am assuming that you are rolling everything into an IRA as you have the option of going into bonds. Otherwise you would be taxed heavily.
Also, liquidity (having quick access to your money) doesn't seem to be your concern since you have thought of bonds. Your money would be locked in for a long period so you wouldn't have access to it.
Based on this: put some in the money market for now while you continue to research what you wish. If you are satisfied with your current stock investments in the long run keep them. If there are other stocks or funds that you have been advised are providing greater returns, then take them. Traditionally, stock markets have outperformed bond markets.
Here is a good article to start:
Fool.com's article on rolling over to an IRA
