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Above is a graphic I jimmied up comparing the Monster Tables for Dungeon Levels 1-3 from OD&D Vol III (Jan '74), the Greyhawk Supplement (Feb '75), and the 1st three printings of Holmes Basic ('77-'78). I reoriented the tables for side-by-side comparison. I didn't have a scan of the 3rd print Holmes Table handy so I just annotated the changes. The Holmes table doesn't change again after the 3rd print. The obvious absence is the tables from the Monster & Treasure Assortment, Set 1, but with 100 entries for each level it wasn't practical to include it.
As you can see, the table from the 1st print Holmes has the same number of entries for each level as in Greyhawk, and preserves many of the monsters. The 1st level Holmes table actually includes every single monster from the 1st level of Greyhawk, with a few additions crammed in. The 2nd level of Holmes diverges more, and includes a few real oddities: Leprechauns, Troglodites [sic] and Piercers, monsters that appeared nowhere in an OD&D rulebook or Holmes itself. Leprechauns and Piercers made their debut in the Strategic Review #3 (Autumn '75), and Troglodytes in the convention version of Lost Caverns of Tsojconth ('76). As I mentioned yesterday, these monsters also appeared in the tables in the Monster & Treasure Assortments, so that may be the reason they ended up here. The 3rd level table preserves at least half of the corresponding Greyhawk level, and includes one more monster that debuted in the SR #3, Shriekers.
The tables in the 2nd print (Jan 78) of Holmes attempt to "fix" the tables for Basic by removing monsters not described in the monster list, and NPCs over 3rd level, also not described in Basic. Lower level NPCs were retained. One missing monster was overlooked (Gnolls), so in the 3rd print these were also changed - but they also went ahead and removed all of the classed characters. The changes are not especially imaginative and reduce the variety found in the tables, resulting in duplicating entries for bandits and orcs on Levels One and Two.
Ironically, the 2nd edition of the Holmes rulebook altered the Monster List, adding in a bunch of low level monsters from the Monster Manual, including many of the missing ones from these tables - Giant Rats, Giant Centipedes, Large/Huge/Giant Spiders, Gnolls, Troglodytes and Shriekers. But these monsters were never given their places back in the Wandering Monster Table.
2/2016 Update: The 1st printing of OD&D Vol III had a slightly different list for Level 2. Entry 7 was Ghouls rather than Thouls, and entry 8 was Toads rather than Ghouls. This must be the source of the Giant Toads in the Level 2 lists in Greyhawk and the Holmes 1st printing.