Hi there
Well, in theory, most if not all of the "strength" or your links will pass on to the new site if you use a 301 redirect. We've had a recent Matt Cutts video talking about this.
In order to streamline the process, I would replicate an identical site structure on your new .com site. Same /sub-folders/, same primary article names, as similar as you can make it to you .net domain, the better.
This will allow you to 301 redirect the old domain to the new one, pointing the equivalent pages and sub folders to each other - so domain.net/sub-folder/ to domain.com/sub-folder/ and domain.net/article1.html to domain.com/article1.html. This way not only are you ensuring that the user is following the same path as before, but all of the "strength" and previous links are being pointed to their new, equivalent pages.
It's such a big help if you can keep the site structure the same. Now, there may be a case for not wanting to redirect everything - thousands and thousands of 301s can slow down the .htaccess file, not to mention the time it may take. Some pages may not be worth transferring anyway if they have no link juice or are never visited by users. In this case, it's perfectly acceptable to let these return a 404 error.
If you're looking to get the URLs you want to redirect on bulk, look in your XML sitemap. Download that and extract the URLs from there and place them into Excel. Most of the time the listed pages will be the ones you want to redirect. Copy the list into another column, so you now have 2 identical lists. Then simply use the Find & Replace tool on one of the columns, changing .net to .com. You've now got all the URLs you'll want to put into your .htaccess file for redirecting.
Finally, it wouldn't hurt to contact some of the webmasters on the sites where you have your best links. If you tell them you've moved to a .com domain and only that needs changing, they can do the leg-work for you and can ensure that your new domain keeps its strength.
Hope this helps - good luck with the move!