Deeper Commentary

Psa 99:1

Yahweh reigns! Let the nations tremble-
This appears to be a Psalm rejoicing at the prospect of the restoration of the exiles; the Gentiles were to tremble in repentance, so that they too could join in this program. The ideas are very similar to those in Ps. 97.

He sits enthroned between the cherubim: let the earth be moved-
There was envisaged a dramatic theophany which would be associated with the fall of Babylon and the restoration of God's exiled people. The cherubim which Ezekiel had seen departing from Zion would return. But this isn't what happened; Judah in exile didn't really repent, and those relatively few who did return were clearly motivated by the hope of personal benefit rather than the glory of God. Babylon didn't dramatically fall as envisaged in the prophets, there was no theophany; so much potential was wasted. But these things are rescheduled and reapplied to the final restoration of God's people at the last day. 

The commands concerning the tabernacle were given to Moses by the Angel- do phrases like "Let them make Me a sanctuary; that I may dwell among them" (Ex. 25:8) have primary reference to the Angel speaking the words? In the same way, does Psalm 99:1 refer also to the physical presence of an Angel between the cherubim? Similarly "Give ear, O Shepherd of Israel (the Angel- so Isaiah 63 describes the wilderness Angel), thou that leadest Joseph like a flock (the Angel lead them through the wilderness); thou that dwellest between the cherubims, shine forth" (Ps. 80:1 AV). And again in Ps. 20:1,2 "The God of Jacob (i.e. the Angel who Jacob recognized had been so much in his life) defend thee; send thee help from the sanctuary... ", as if it was in the sanctuary (Holy Place) that the Angel was located.
The four cherubim covered the ark, over which dwelt an Angel; Ps. 99:1,7 therefore describes the Angel as dwelling between the cherubim: "The Lord reigneth... He sitteth between the cherubims... He spake unto them in the cloudy pillar: they kept His testimonies, and the ordinance that He gave them". These latter things were all done by the Angel. Also relevant is Ps. 68:17,18: "The chariots of God are... thousands of Angels; the Lord is among them, as in... the Holy place". One Angel, which dwelt in the Holy Place, was therefore central to those thousands of others. See too Is. 37:16,17 on this. Similarly, Isaiah saw "the King, the Lord of Hosts (Angels) sitting between the cherubim" (Is. 6:5). The phrase 'living God' may mean 'the God of the living ones', and would therefore describe this mighty Angel- it is linked with "the Lord of Hosts" (Angels) in Jer. 23:36 and the Angel that dwelt in the temple (Ps. 42:2).

Psa 99:2

Yahweh is great in Zion, He is high above all the peoples- Because of God's grace to Jacob / Israel (:4), an undefined group are bidden come to Zion, to the very cherubim (:1; in the Most Holy Place) to exalt and praise God at His footstool. This group, in line with the preceding Psalms, are surely the Gentile world. "Let them praise Your great Name" (Ps. 99:3) would surely make most sense if it referred to the Gentiles, seeing that David or the Psalmist was Israelite. See on Ps. 96:7.

Psa 99:3

Let them praise Your great and awesome name: He is Holy!-
The "them" are the Gentile "peoples" of :2. Perhaps the triple command to 'Sing to the Lord' in the opening verses of Ps. 96 alludes to Israel's three feasts, as does the triple, repetitive verses of Ps. 99:1-3, 4,5, 6-9; which likewise bid the Gentile world to come to Israel's worship. See on Ps. 96:7.

Psa 99:4

The King’s strength also loves justice; You establish equity, You execute justice and righteousness in Jacob-
This looks ahead to how things will be at the final judgment: "He comes to judge the earth. He will judge the world with righteousness, and the peoples with equity". This is quoted in Acts 17:31 concerning the final day of judgment at the Lord's return. But right now, justice and righteousness were to be executed and to be the basis of the restored Kingdom. For the essence of the Kingdom is now.

Psa 99:5

Exalt Yahweh our God, worship at His footstool. He is Holy!-
The ark is called both the throne of God and also His footstool (Ps. 99:5; 132:7,8; 1 Chron. 28:2). Above or sitting upon the cherubim, the pagan mind expected to see Israel's God. But there was (to their eyes) an empty throne. Yahweh had to be believed in by faith. And His supreme manifestation was through the blood of sacrifice. Cassuto gives evidence that the Egyptians and Hittites placed their covenant contracts in a box beneath the throne of their gods; and the tables of the covenant were likewise placed beneath the throne of Yahweh. This similarity begged the comparison yet stronger- Israel's God was not seated there. He had to be believed in by faith. Such a concept of faith in an invisible god was quite foreign to the pagan mind; and yet the whole tabernacle plan was designed to have enough points of contact with the pagan tabernacles in order to elicit this point in very powerful form: the one true God is invisible and must be believed in.

Psa 99:6

Moses and Aaron were among His priests, Samuel among those who call on His name; they called on Yahweh, and He answered them-
The Psalm invites the Gentiles to make Israel's God and history their own. For :5 was an invitation to the Gentiles to accept Israel's God. The Gentiles who chose to call upon Yahweh's Name (:3) would therefore be identified with Samuel and the great heroes of Israel's history. This of course was not what a proud and nationalistic Israel wanted to hear.

Psa 99:7

He spoke to them in the pillar of cloud-
As God miraculously led Israel out of Egypt and to the promised land, so He was willing to use miracle and power to lead His people out of Babylonian exile and back to the promised land. But they were unwilling.

They kept His testimonies, the statute that He gave them-
This was likewise required of the exiles. The "they" could refer to Moses, Aaron and Samuel- but the "them" in the context is the "them" to whom God spoke in the pillar of cloud, who were given God's law ("the statute that He gave them"). That group didn't include Samuel, who lived centuries later.  The "them" is the group whose sinful works are to be judged by God, albeit in mercy (:8). The "them" is surely Israel- and this is in line with God's imputation of righteousness to His people, not beholding iniquity in Jacob, because He so loved them (Num. 23:21). This is as big a problem for us to get our heads around as are the NT references to our appearing [Gk. 'being presented as'] faultless before the presence of His glory... without spot in His sight.

Psa 99:8

You answered them, Yahweh our God; You are a God who forgave them, although You took vengeance for their doings-
This was to be true likewise of the exiles. Forgiveness would be possible, but they had to accept that they were being punished for their sins. Ezekiel records how they insisted they had been punished wrongly and unfairly.

Psa 99:9

Exalt Yahweh our God. Worship at His holy hill, for Yahweh, our God, is holy!-
This is an appeal of the repentant Jews to the Gentiles, to come to Zion and worship our God. The Kingdom prophecies of the nations flowing to Zion could have had some fulfilment at the restoration. But the Jews weren't that devoted to Zion, and initially continued worshipping Gentile idols; and became proud and xenophobic rather than acceptant and welcoming to Gentiles.