there are many sources for indo-europian languages' etymology but I don't know where to find one which shows the pronunciation of the word's origins. for example, I can't understand how the given greek or old germanic words are pronounced.
Wiktionary, for all its (usually overstated) flaws, very often has IPA for entries; in the case of Greek, it usually has pronunciations for several different time periods, even.
Greek, specifically, has a very phonemic writing system, so once you get a handle on the phonology of the language the pronunciation of more or less any word is very transparent. Any Greek textbook will have a section on phonology, and if you want something a bit more thorough but still very accessible, W. Sidney Allen's Vox Graeca is excellent.
The spelling of reconstructed languages like Proto-Germanic is almost always perfectly phonemic—that's the point. The exact phonetic realisation will often be in doubt (at least more so than for Greek), but again, familiarity with the phonology and with the conventions of the specific language will get you a long way. Wikipedia will often have an adequate introduction, e.g. Proto-Germanic.
At the risk of sounding obvious, if you want to know how words were pronounced in a given language, you will need to acquire at least a passing familiarity with that language.
Since you tagged the question proto-indo-european, I'll also add:
The pronunciation of reconstructed proto-languages is always somewhat uncertain, and the older we go, the less certain we can be. For Proto-Indo-European, there's no real consensus about how it should be pronounced: were the "voiced" stops glottalized, perhaps ejective? Were the "voiced aspirated" stops actually aspirated? Were the "velar" stops actually post-velar, or maybe uvular? Was *h₁ a stop or a fricative? And so on.
For most scholars, this doesn't really matter, since there's no real reason to actually speak reconstructed PIE. But as a result, there tend not to be any good pronunciation guides for it. If you want a way to pronounce it (maybe as a mnemonic), you'll need to pick one of the many, many theories; personally, I'm a big fan of ejectives and uvulars, but none of the theories are without problems (for my favorite theory: so where did the ejectives go?).