Seriously... I hear a new giongo almost every day it feels like. A couple of days ago my wife and I walked past a baby that was sort of fidgeting and she said 赤ちゃんもぞもぞしている。I was like.....what's もぞもぞ？ I swear... there must be thousands of these things.

Anyone out there actually mastered giongo? Harder than kanji in my opinion haha.

Nope.. I have like 10-20 i use actively and wing the rest when I hear them.
I heard ぽくぽく the other day for the first time, and I asked a friend of mine what the hell and she was like "木魚を叩く音やで!" and looked at me as if I should've known that. I didn't even know what a 木魚 was, so I had to google that first, haha

There's a book called 日本語擬態語辞典 by 五味太郎. I have a copy of the book and intend to go through it in Anki at some point, but that's for after N1 for me.

Relevant thread:
http://forum.koohii.com/showthread.php?tid=3078

*Edit: I guess giongo, giseigo and gitaigo are different, so apologies if you meant giongo specifically.

I rely solely on context for those I haven't learned yet. If it's not used in something like 「＿＿が何々っと＿＿」 or otherwise given context, I have no idea...
When it's used like a verb, I have to look it up if I want to know.

[Zgarbas]

I usually just get them from context. onomatopoeia are my favourite sounding Japanese words*, but for the life of me I can't remember them.

*srsly, whenever I hear one I'm filled with this temporary burst of joy.