Well, you should already know if it's for PAR(Pro Action Replay) or Gameshark, when you get the codes, it should tell you what they're for.
As for the "V3". I find it best to just use v3 for all of them, and if they don't work, go back and change to v2 or v1. V3 seems to work most of the time though.
If it's a gameshark code.. You use "gameshark_v#".. if it's an action replay code, you use "PAR_v#"
So, example from that link you gave.
PAR_V3 Master Code(M)
72bc6dfb e9ca5465
a47fb2dc 1af3ca86
8d671fd9 6f6beff2
78da95df 44018cb4
6b5aeec6 f80e49bc
1c7b3231 b494738c
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