Here's how I set it up...
1. Name and Reward.
Don't forget to put your name and contact information inside the front cover. Include a "Reward if returned" statement. If you wind up using it and lose it, you'll want someone motivated to get it back to you.
2. Number every other page, bottom right hand corner.
Numbering allows for easier reference (see below). There are 240 pages in my journal, my first numbered page is 3. Odd pages only because I'm too lazy to write on every page, and numbering the even pages as well is unnecessary.
3. Index in the back.
Take the last 10-20 pages to create an index. There are some things you will want to reference again, and some projects will wind up in more than one place in your journal. You can list the content you'll want to access quickly in a variety of ways. I have my index set up on pages 230-240 with a "Sermon index" separate from the general index.
4. Tape a calendar inside the back cover.
Print out a small, year at a glance calendar and tape/glue it inside the back cover. It will come in handy.
5. Use the accordion pocket in the back.
Some people keep an extra $20 in there. If I had an extra $20 maybe I would do the same, but I'm not even sure what an "extra $20" is. I keep a few 3x5 cards in that pocket for scratch paper, writing directions for people, etc. and a few business cards.
6. Get a good pen/pencil.
By "good" I do not mean expensive. I mean get a pen that wont smudge, or use a pencil. I prefer a thick pencil lead (0.9 Pentel Twist-Erase). It just feels right, and I need to erase.
I am always looking for other ideas and would love to hear what you do with a Moleskine. I saw a number of men using them at the Chicago A29 Bootcamp, so if you use 'em, let's hear about it.