Most genealogy programs have implemented the basic connections between people and families and the basic events and facts of the GEDCOM standard. You are usually safe with entering the standard data that most programs accept.
It is where you are dealing with more advanced features of your program where you will often have problems. If your program does something that many other programs don't do, or don't do the same way, then it is very likely that not all the data entered via that feature will transfer to other programs properly.
The most often reported set of data that usually will not transfer between programs are the citations for your source references. Programs that implement citations often choose the Mills templates, but they are not perfectly defined and each program implements them with slight differences. But worse, GEDCOM was written before citations were implemented extensively in genealogy software, so each program has invented their own way of writing citation information to GEDCOM, and few programs have implemented input of this custom GEDCOM from other programs.
There are many other data items that are affected by different implementations. The worst problem is an inconsistent implementation of the CONC (concatenate) tag in notes. If you transfer your data between two programs that export CONC tags differently, then you may find that your notes have extra spaces in the middle of a word every line or so, or may have the space between a word missing every line or so.
Your best bet to minimize these problems is to use a program that says it exports its data to GEDCOM using the 5.5.1 standard. The program should then only allow you to enter data that can be exported. And programs that say they can properly read in GEDCOM 5.5.1 should then be able to read in most of the data - at least the parts that they've implemented.
It does also future-safe your data, because any future standards that are written will have to make sure that GEDCOM 5.5.1 conversion programs will be available.