FYI , actually "wae", "ae", and "bae" is the same. The correct spelling is "wae". But Javenese, like most of Indonesian, tend to pronounce words in short & easier way (and even write them exactly like how we pronounce it though they're wrong.) so we often write "wae" as "ae", some dialect use "bae"
I slightly disagree with yudpray. While obviously "wae" means "saja" in Indonesian. But "saja" is not always "wae" in Javanese. Since "saja" can means "only" in "English" but I think "wae" will never means "only". Javanese had another word for "saja" when it mean "only", it's "mek". But with exception if you say it cynically. :)
So, "wae" have different meaning in English based on your tone. It's used when there's condition comparation.
For example, "Mangan wae." (for your information, "mangan" means "eat")
> With cynical tone "Mangan wae." means that the second person is doing only eat and eat. Literally: "Only eat." (You only eat and eat, don't you have any other thing to do?/Can't you stop eating?")
Here, you are emphasizing that there's better thing for him/her to do than just eating all the time.
> With normal tone, "Mangan wae" means that you are stating that you (and the second person) should eat. More or less like "I (We) better eat." (Let's eat.)
Here, you are emphasizing that eat is better than doing the other thing.
And yes, "sae" is an adjective which means "good" in terms of quality. Whether it's about health, condition, etc.
"Sae" is the polite form (krama) of "apik".
> Aku sae = I'm good. (not about you're good at something, but your condition is good.)
> Radio punika sae = That radio is good