I am a new CM consultant (less than a month), but have been scrapping for 3 + years and my books over the years have used a lot of other papers and stickers.
Buffered basically means that the paper has been treated to help prevent acids from other sources (pictures, memorabilia, your fingers, other inks) from migrating through the paper to your pictures.
As far as markers and pens, I pretty much use Micron pens produced by Sakura. These are the pens that Creative Memories used to sell. I am not sure if these are still the pens that they sell but with their name on them or not. I do know the ones I bought 3 years ago from Creative Memories ARE Micron pens ( and I haven't needed to replace any). These are the same pens used by Quilters (my mom is a big time quilter in a guild) to sign their quilts. You can get them at Michaels, and many other stores if you want colors other than what CM sells .
When I have used other "contraband" product
in the past 
such as stickers and / or paper, I have made sure that it does not come in contact with the pictures. I pretty much keep away from putting any stickers on the pictures themselves regardless of whether they are CM or not. There are definitely a lot of stickers out there. Quite frankly I own a bunch of them. I bought a TON of Mrs. Grossmans when CM was selling them (from Hobby Lobby

). As for the safety of other brands, I just don't know. Like I said, I tend to not use any stickers on my pictures regardless of who made them. When I have used others (Me and My Big Idea, Sandylion Disney Stuff, etc...) they have always been placed away from the picture.
Keep in mind, the more paper you put on the page (e.g. wallpapering the pages) makes the pages and the books themselves heavier. I try to limit the wallpapering, or reduce the pages in the book when I do it. In fact I do a lot of picture wallpapering, where I basically completely grid the layout with lots of pictures with a little bit of colored paper as accent. Talk about heavy!!!!
As far as glues, I ALWAYS use Creative Memories tape runners. Yes I have bought others, but not found anything I like nearly as well, nor that I feel comfortable with. The tape runners are comparable with most of the other "tape runners" on the market in price, and quite frankly I think they rock.
With regards to other memorabilia, I either put the stuff in a separate photo mounting sleeve, or I tape it down with the tape runner, mounted on CM paper, or the book, and make sure it does not come in contact with any pictures. Since I use the page protectors, that is pretty protected. For newspaper articles, copying them onto special paper, and then mounting them is really the way to go, as the newspaper will yellow considerably. I do not use the archival mist. I haven't looked at it really closely ever, but I do not want to spray anything onto my memorabilia. I would much rather use the clear plastic sleeves to protect them, than to take a chance of it affecting the memorabilia, or ruining something. Others have used it and had luck, and it may be fine, I don't know. I am paranoid however. I actually freak a little about digital photos printed on the CM paper and let them dry forever before using them, and then immediately put a page protector over them before ever closing the book.
As for OTHER THINGS. I personally cannot vouch for the eyelets and or wire used in scrapbooking. I am not concerned on the acid free, archival side of things. I am just thinking that is a big hunk of metal or hard plastic, etc... in the book that will over time leave some sort of impression on other pages or tear something there. That may not really be the case, but that is what keeps going through my mind. Paper meets metal, wears through. I don't know. Adding too much poofiness to individual pages also concerns me a little, does it limit the amount of pages in a book? Are there problems with the page protectors?
I hope this info helped somewhat. Good luck.