Multi Site Linking Do's and Don'ts HELP!

So I've got a bit over 200 sites in several different niches, and am trying to figure out what the rules are for linking between them.
I've searched high and low in the form and online but all I've found is site "interlinking" on one site (meaning a site linking to itself throughout the pages). That's not what I'm trying to do.

Here are the details:
- Over 200 sites
- Approx 115 diff C class IPs
- Each IP has 1-3 sites attached to it (never more)

All I know is that you should NEVER complete the circle (e.g. Site 1 --> site 2 --> site 3 --> site 4 --> site 1) and that linking sites with the same IP to each other should be avoided (e.g. site 1 on 100.100.100.1 can link to site 1 on 100.100.100.2, but that site 2 on 100.100.100.2 should not link back to a site 1 or 2 on 100.100.100.1)

I hope all the makes sense =p

Anyway, so what I need to know is are there any other "rules" or suggestions when it comes to linking sites to each other. What are the do's and dont's of linking sites.

I'd also like to know if there is a good way to organize all this to a) make sure I don't repeat IP's and complete circles and b) to help keep me SANE!
Right now I'm just using excel but the lists and spreadsheets get a bit to large to manage easily. Maybe there is some sort of software or something?

BTW I am doing the linking in the footers of the sites, and trying to keep the links relevant to the page it's on.

Any and all help or advice would be much appreciated!

Thanks