In search of a clear answer to this question, I did some googling. I didn't find anything particularly concise on this site, but I did find this description that was particularly helpful to me. Forgive me if you all knew this already, but I've been primarily an acoustic guy for my playing career, so I wanted to know!

From http://www.guitarsite.com/guitar_FAQ.htm#LOOP

"What is an effects loop?

Effects loops give you the opportunity to plug effects between the preamp and the power amp. This is best for modulation (phaser, flanger, chorus, pitsh shifting) and delay effects because it allows them to effect the distorted signal as opposed to the preamp distorting them. It also runs a line-level signal, instead of instrument, which works better with most rack mount effects. (Distortions and boosters, etc, usually work better going straight into the guiatr input where they can affect the preamp gain)

Most have output jacks that run to the effects and input that run back to the amp. Regular guitar cable is good to use for these jacks. A few have one stereo jack that has both input and output and require a stereo-plugged "Y" guitar cable with one cable running as the input, one as the output.

Serial effects loops rune directly between the preamp and power amp, parallel ones allow you to mix the "wet" loop signal with the "dry" preamp signal.

You may also run the preamp signal out of the effects loop into the effects input of another amp to get a "slaved amp" effect or just to use different preamps with different power amps.

There is no "wrong" way to set effects up before the amp, in the effects loop or both. You just have to experiment with what you like best. Many effects, wah and chorus for example, will sound more dominate in the effects loop. This could be desired or not. I run my wah and Micro-Vibe into the guitar input (slightly overdriven for rythym), because I like how the preamp's O/D softens, or delutes, each of them. I keep my O/D and Fuzz pedals before each though, so the wah and Vibe and affect and fatten the fuzz tones. I keep my chorus and echo in the effects loop both because I like the way the affect all that comes before it, but also because they are both picky vintage pieces and work better with the line-level signal.

The more distortion the effect runs through afterwards, the more the effect is lost in the finished tone. "

I hope this is helpful for some people.
Quote by roshjosh
What pedals are better to plug into before the amp than in the effect in/out on the amp?

Are you asking about a specific model of pedal? I'm a little confused because I feel like this is answered fairly well in the quoted post.