Temple was my least favorite for a long time, but in recent years, I think it's completely reversed itself in my ranking of Indy films. In light of the last two movies in particular (LC and Skull) TOD sets itself apart by being the most dramatically different in premise and formula than the others (even if it does adhere pretty closely to the established Raiders formula, it does so in a way that seems much fresher and more original than LC and Skull.) In addition to the much more original feeling setting, story, and tone, the Thuggees just kick so much ass as bad guys that they pretty much make the film for me. I mean, here is Mola Ram, one truly bad dude, using black magic to brainwash the innocent and ripping people's hearts out before slowly lowering them into pools of molten lava. Can you say "friggin' sweet?" Heh, seriously though, I just love the movie's great mix of horror, humor, and action, and I love the fact that it, more than any of the other Indy films feels like a true homage to the genre (see the raider.net article about TOD and Gunga Din.) Not to mention the fact that Indy himself is more of a blatant badass in TOD than in any other movie. In LC, he's a lot more reserved and professorial. In Skull, he plays the aging mentor. Even Raiders has him more balanced between professor/digger/adventurer. But in TOD, he's fending off hoards of Thuggees with fists and a giant bowie knife, muscles rippling, shirt in tatters--it's classic pulp fun, and I love every second of it.
What it really boils down to, for me, is that of the four films, TOD feels the freshest and most original, not to mention the most pulpy and exciting. I was born between Raiders and Temple, and I didn't really get into Indy till Last Crusade came out in '89, so I never had the experience of seeing Raiders by itself and having it be the be-all, end-all of adventure movies. For that reason, I feel like I have been able to judge the movies on a different set of merits--they were just amazing fun and filled me with wonder when I was a kid, and my favorites nowadays are basically whichever ones give me that sense of giddy excitement that I got when I used to watch them as a child. Right now, TOD does that the most for me.