I'm currently making an animation on milkshape and I was wondering how do you flip the skeleton so it's not facing the front it's facing the side. Also are there any programs or plug-ins that I can install to make milkshape easier to use?

I'm not certain I'm understanding you correctly but if what you're trying to do is turn the rig in another direction you select the b_ROOT_bind joint and then use rotate.

As far as I know there are no programs or plugins you can install to make animation in Milkshape easier. Milkshape really isn't the best 3D editor for the job in my opinion. If you're willing to try something new give Blender a try. That editor is free, gives you a lot more control while you're working, and the tools/rigs available for Sims 3 animation with it are superior to the ones currently available for Milkshape.

You unhide skeleton(and mesh)
Select all
Go to Animate and choose rotate all
fill in 90 degrees in the y box
hit ok

I dont have seen many animations but aren't they all based on one and the same starting position?
Rotating the skeleton isn't then the way to go i think but rotating the slot were the animation starts might be a better option?

I would not suggest selecting all the joints. There are some that if you select them your animation could become distorted in the game. Best to just rotate the whole rig using b_ROOT_bind.

Depending on what you want your animation to do making the sequence start from the idle position could be helpful. You don't need to move slots or anything to do that. Just start with that clip, use it as the base for yours, and be sure to remove the IK if you're using MS.