Looking at your original question about registering web 2.0's in your name or your company's - doesn't matter for ranking but it's a question of your goal: are you branding? Are you just trying to manipulate rankings?
If the latter, it doesn't matter who you register under. If the former, probably your company's name. But it's not as if you can't build the web 2.0's - they're links to get all the same.
As for what to do instead of link wheels - I'd start with finding your top competitors across tough terms, as well as consistent competitors across your long-tail KW's. Mainly you want to find the sites that are ranking for the tougher terms, and follow their best and strongest links if you can. Since you're posting in the SEOMoz forum you can start with the SERP analysis functions of the keyword research tool.
I also use other tools to find competitors across niche related keywords (A1 Keyword Tool from Microsys is one): but you want to find quality competitors and not just copy anyone online: you could be copying a link profile of a poisonous website and repeat their mistakes.
That's why I'd start looking for those sites that rank for the tougher terms. Find their best links, try to copy them.
Link acquisition is more than copy-cat SEO, though - you can read plenty more about it in the forum or YouMoz blog, or one of Rand's many posts on the matter of link building - but I'd suggest looking at making your site(s) capable of attracting links, finding raving fans of your brand and give them incentives to share your content (i.e. build links - like running a contest for instance), creating awards for other websites that are somehow correlated to your site and getting a link via the award (an older but effective method)...
I'd run from the "flavor of the month" methods like link wheels because it's not going to net you quality and sticky links. Those links will have a high amount of link rot and are designed to provide the link wheel company/software provider with a recurring income, meanwhile in today's environment you'll simply be out-running and inviting Google's manual review (especially if a competitor decides it's best to rat you out in Google Webmaster Tools: link wheels are easy to find).
When your site drops rankings, the answer is always going to be, "build more links," or "use another tool," or "you did it wrong, but keep building more links to replace the links you've lost." Meanwhile it's time and money down the drain.
Solution: build a defensible link profile.
Go for the links that are harder to come by because your competitors are too lazy to try: they're all busy with link wheels.
Think of it this way: the PageRank/link juice of a link is calculated on a logarithmic scale. It's much harder to get a PR 6 link than 100's of PR 1 links. The site that gets the former is going to out-rank the site floating on the latter, and it's just a matter of time before the temporary rankings generated from the cheaper methods get penalized or otherwise demoted by the algo.
But experiment: all this is just my experience. After Penguin I've had to rethink everything, but I was one of the loudest mouths supporting link wheels and everything else "that worked..." That short-sighted pragmatism wound up biting me in the end.
You might find something in your experimentation that I totally missed, but I don't want the responsibility of giving out more bad advice, so I'm more cautious in what I share these days.