I am not sure it is really an operating system compatibility issue. Hard drives come in a variety of interfaces, and not all interfaces are compatible with all systems. These days, most hard drives use SATA or SATA II interfaces, which have different types of data and power connections than legacy IDE drives did. If you have an older computer, that may be an incompatability, although there are adapters (I don't really recommend adapting, however.)
What may be a bigger issue when buying larger, newer hard drives, is to make sure that if they use SATA, that your system supports the version of SATA used. Most newer computers support SATA I and SATA II, however there is a SATA III standard that is very fringe, and care should be made when buying high-performance SATA drives. While a SATA III drive can be used with older SATA II systems, you will not get the top-notch performance that full SATA III compliance will offer. This is particularly an issue if you are looking to buy top-end, high speed SSD drives.
Beyond the possible physical compatibility issues, given how old Windows 2000 is (and possibly XP), you may need to make sure your system is fully patched with the latest Service Packs and updates to use SATA drives.