I have looked around to find nothing really usefull pertaining to this question.
When it comes to using amp sims, is it better to record clean then add effects, or just to record with the effects already in?
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if you do it with the effects already added you know exactly what it will sound like.

id rather dial the sound i want in first then record it instead of doing it the other way around

thats what steve vai does, if its good enough for him its good enough for me.
Record exactly what you want people to hear. You should only make minimal changes afterward.
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It depends on the effect. Usually I'll set anything that effects the sound of the guitar (Distortion, Overdrive, EQ, Wah, Pitch Shifting) then record. I'll add modulation effects (Chorus, Reverb, Delay, Filters) afterward unless I'm doing some crazy U2ish riff.
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it depends. this is, once again, one of the situations where you have to do what is best for the song. if you are doing a U2 type delay (like lock suggested), you will have to record while at least monitoring the delay. there is a huge interplay between what you are playing and the effect. if you are just adding some subtle delay to a solo for depth, add it later.

even with amp sims, ill sometimes just record completly dry. this really only works well on clean parts, or at least for me. even if i dont know exactly what i want the gain to sound like, its better to have some sort of distortion/overdrive going so you have some idea what is going on in that sector.

Quote by seemeel
Record exactly what you want people to hear. You should only make minimal changes afterward.

i completly disagree with this. the whole point of doing things digitally is that you can make drastic changes later if you need to, but still have the original signal. i change amp sims, modulation plugins, etc. all the time to find what works best. even when reocording an amp, i first start by getting the best sound i can for the "dry" amp, and then work on the effects.
at one point in time it may have been best to record everything exactly as you want it to end up, but in this day and age that is extremely limiting.