I cant say it does, but when I changed ips i had a drop in rankings. But i cant prove it was the change in ip
but there is some logic to it,
A domain name is resolved to a ip address to find the website, the domain name is sent in the header. Your web site accepts a connection on a socket, ip number and port 123.123.123.123:80, it then looks in the header for the domain name
so a SE will see a difference, it will know this is not the same address

1. you need to make a change to your DNS settings.

where every you registered your domain, you ned to change your Arecord to point at the correct ip number

2. you need to do a 301 redirect to primary domain.

If it was a windows server, i could of written the rule for you,

yes time consuming, rrom for error, and you will lose some ranking from 301 link juice leaks. but beter to do it now then next year

Zsolt makes some good points

It not a problem, it’s a natural thing to do.
As far as PageRank goes if you link to every website from every website it will have neutral effect over all, but your worse ranking sites will get a boost at the expense of the higher ranking sites. You can alter your links to benifit a site you want to give a boost

But since there is value in link text relevance, you should come out on top all over
Having said that it’s better to link in a way that looks natural to your users.

I would not have these as my only links if they are on the same ip number, but as long as you have a good range of links from other places it is ok to have links from the same ip number. i think people get a bit excited about same IP or same C-class.

Well if you are keeping the link structure it would easy.

you easly do somthing like replace oldomain.com/folder to newdomain.com

What sort of server are you using?

Many say that sub domains are sperate, but i have never seen any evidence for this. i have used subdomains and find that they act just as sub-folders. Matt Cutts has said using sub-folders of sub-domain is a matter of personal chioce.

But many people have been moving their duplicate content to subdomains to aviod the panda update effect. I have no idea if this works to protect the root domain long term or at all, it just may take time for google to find it and call it as duplicate again.

i would go with the .net myself, why risk it, time is money.

As for the 301's, if you are keeping the same site structure then you can ddo this with one 301 redirect, if not I would go to WMT and find the pages with incomming links and 301 those pages only, there is nothing to gain from 301ing pages with no links. Ok maybe someone has a url bookmarked and may not find your new site, but it not too likly thats going to be a big problem