To supplement Nick's excellent answer:
The mainstream view of PIE now is that it had no /a/ vowel (in the oldest stages we can reconstruct). Instead, it had three(*) "laryngeal" sounds, which weren't actually particularly laryngeal, but the name has stuck. They're conventionally written *h₁ *h₂ *h₃ and there are various theories as to their actual pronunciation: personally, I like the idea that they were /h x ɣʷ/, but there's not enough evidence to be sure.
(*) Some people suggest that there were four or even five, but this hasn't caught on.
But in every Indo-European language known at the time(**), these "laryngeals" never appeared directly. Instead, they only appeared as a "color" on the surrounding vowels. In other words, *h₁ *h₂ *h₃ first affected the surrounding vowels, then disappeared entirely.
(**) Hittite was discovered after the laryngeal theory was proposed, and did actually show direct evidence of some laryngeals. Which adds quite a lot of evidence to the theory.
In particular, *h₁ turned *e into *e (no change), *h₂ turned *e into *a, and *h₃ turned *e into *o. If the laryngeal came before the vowel, the result was short; if it came after the vowel, the result was long.
So Wiktionary is showing the (more modern) reconstruction of older PIE, while the laryngeals still existed, and Etymonline is showing the (older) reconstruction of later PIE, after Hittite split off and the laryngeals vanished.
Note, as the others have said, that Etymonline is also ignoring several important distinctions in PIE: *ǵ and *g are separate phonemes in every reconstruction I've seen, and there's significantly more evidence for them than there is for laryngeals. (See the centum-satem division for examples.)