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How do I safely transfer seedling plants with true leaves from tiny cups to pots? Also, how bad is it if they have grown taller than they need to be transplanted? For example, some of my seedlings have more than two true leaves and are more than two inches tall...

It will depend on what they are. Why don't you tell us what you have... Possibly post some photos.

But no that doesn't sound too tall. You should be able to just slide your plants out of their little cups with the little root ball intact .

I have peppers with 4 true leaves, some columbines just starting to grow true leaves, and tomatoes with 4-10 true leaves, a few of them are pretty tall...I'll move them tomorrow. I hear I should hold them by the true leaves when transplanting? I'm afraid I'll break the roots when taking them out and damage from separating the seedlings in the same cup.

Peppers grow slow so that should be ok but I don't like to do more than two up pots before going to the ground.

I tend to cradle the rootball at the base of the stem with my fingers rather than dangling them by any of the leaves (longer roots can dangle). If placing in a narrow container that my hand/fingers won't fit, then I use a plastic spoon or fork.

-- taking out -- It's easy with individual cups and containers, just support the top of the soil mix with your fingers spread to gently hold the stem and/or with fingers supporting the soil between the seedlings, then turn the container over so the drop to the work surface (if accidentally spilled) is no more than an inch or so. Sometimes you need to gently tap the top edge of the (upside down) container against a solid surface (which needs to be tall enough so the plant isn't mashed into the work surface in the process).

...I still have frustrating time with cells unless the seedlings are overgrown and rootbound enough to push out from the bottom or thunk loose then pull out by the sturdy stems. I haven't got the hang of using knives or forks.

Good tips so far. Also be advised that you can plant tomatoes much deeper than they were. The plants will send out roots on the buried stems and increase the root structure.