One thing that drives me batty about submitting manuscripts to journals is that just about every one of them has a slightly different format for how they want things. Everything from margins, fonts and how things are referenced/cited to the title page and file format for the submitted manuscript. Drives me nuts.
AIP has a good system going where you can use LaTeX and the RevTeX macros to create your manuscript. All you do is specify the journal you're submitting to in the \documentclass and it's ready for submission. The journal style file takes care of all the formatting for you. Works for all the AIP journals. It's great. Sadly TeX/LaTex remains obscure enough outside the basic sciences that there aren't any medical related journals that I know of (at least none that I would be submitting manuscripts to anyway) that take TeX/LaTeX files. It's a shame really. The more I do with LaTeX, the more I like it. The output that's generated looks so much nicer than anything Word puts out, and doing equations/figures is dead easy. The learning curve is a little bit steeper, but if you can figure out HTML, basic TeX is well within your grasp. Both are essentially just markup languages so there's really not that much to learn.
Honestly, MS Word sucks for creating manuscripts for publication (IMO). You spend all your time making things look right, and then if you take it to another computer where the default styles/formats might be slightly different, everything looks screwed up. Do you fix it? Leave it alone? Hope it looks ok to the journal editor? Will the reviewers ding you for a crappy looking manuscript because their styles/formats have messed up your manuscript?
My ideal world? Every journal publisher would provide LaTeX style files for their journals and accept LaTeX manuscripts, or at least provide MS Word style libraries and/or templates for their journals (like AIP's Toolkit 2000). I think it would make creating manuscripts so much easier.
Ok, I'm done now (can you tell I've been spending all day trying to cram my manuscript into a Word document?).