I've got some services that I'd like to have prompt me on startup to disable them, and then continue starting up normally if no input is given after say 10 seconds. What's the best way to go about this? Can I just modify the init scripts to wait for input and then timeout and continue?
Yes, you can. There is a risk your modified init script will be moved out of the way on upgrades and replaced by a new one though.
On RHEL based systems, you can press 'I' during boot to enter interactive mode. You can then specify, per service, whether it should run or not.