I try to have the images as close as possible to the dimensions they'll be in my Indy doc. If you're placing files that are 50" tall and scaling them down to 3" you're probably going to run in to huge file sizes, depending on your beginning resolution of course. If it's an inch or two either way It usually doesn't bother me too much.

It really doesn't matter. It used to be with Quark (and I believe Pagemaker) that if images weren't at 100% they wouldn't output correctly. But that was with early versions of the software and antiquated RIPs. These days, it doesn't matter that much as long as you aren't taking a 1" wide photo and scaling it up for the cover of a magazine. But, that's not an InDesign issue.

As Cosmo said, scaling up could be an issue. And you don't want to be scaling down a 2gig file for a 2" image either. Close is good.

Your other two questions, resolution and color mode are good ones though.
You definitely should check with your printer what the optimum resolution is for their printing device your design is being output to, and you should ask them what color profile they want you to send your images.

Also if your image is RGB, and you convert to CMYK while creating your PDF, you may get an unwanted color shift. Best take care of profiles while designing, just so you know. Photoshop's Automated Batch function is great for changing a large quantity of photos.

Just remember to save as a copy. Especially if your original is RAW or native RGB. You want to save your originals in that format. Once you change them to CMYK, a lot of color gamut info is lost.