I suppose one of the ways would be checking the file endings. MV has something along the lines of .rpgmv if they used the encryption. Other than that, once you played a couple, you will be able to recognize engines by their assets for most games.
If the game has an LDB, and LMT and some or even lots of LMU-files, it is made in RPG2000 or RPG2003. RPG2003-games usually but not always have extra-folders that are named Battle2, BattleCharSet, BattleWeapon, Frame and/or System2, depending on what they need and how they were packed for distribution.
RPG_RT.exe can in most cases be the most clear identifier if the icon wasn't replaced:
All but the first of these four categories often have a version-information in the EXE which should tell you more about it.
If the game has the folders Audio, Data and Graphics written with a capital-letter at the beginning, it's very likely it is made in RPGXP, RPGVX or RPGVXAce. In most cases, RPGXP can be excluded when there are folders named Fonts and/or System.
Most the time, creators leave their project-mainfile (which doesn't contain any crucial data) in the game, you can identify it by its filename-extension (RXPROJ=XP, RVPROJ=VX, RVPROJ2=Ace), similar goes for the format of files inside the folder named Data (RXDATA=XP, RVDATA=VX, RVDATA2=Ace). If the game is packed with RGSSAD, you can identify the version by the encrypted game-package's filename-extension aswell (RGSSAD=XP, RGSS2A=VX, RGSS3A=Ace).
In Game.ini, there is a DLL referenced that tells you by name which RGSS-version is used if it wasn't just renamed, most likely it also fits the RPG Maker the game was made in (100~105=XP, 200~202=VX, 300~301=Ace). Game.ini in RPGXP lets you define 3 RTPs, only one in VX and Ace. There should be a Game.exe, which if the icon wasn't swapped will look like this:
RPGXP RPGVX RPGVXAce
There may also be RPGXP-games using the RGSS3-engine and thus utilizing Ace's RGSS3-player to properly run it.