If you have a website which is somewhat matured you are already reducing the risk. There are a number of considerations to take into account in the current search climate the first being link graphs...
Google will have on record the link graph for your website. It uses this a sort of benchmark, if you have previously not accumilated many links you will want to change your graph slowly by adding a smaller number of links in the first week. Once many of these have been found (crawled/indexed - another story altogether) your websites link graph will begin to alter and therefore will be in a position to accept many more links in G's eyes without fear of penalty. As you start to build more links your graph shows a measured upward trend and you can then begin to pummel serious amounts of links because it appears natural (you are popular).
The second aspect is your content graph and how often your content is updated. The content graph is very much the same as your linking one in that G knows how frequently you update content. How would it seem to you to throw thousands of links at a website which has not been updated in months? unnatural? quite.
So, combine these two measures when considering building serious amounts of links to your website. Update the content a couple of times before building any links if your webiste has been left to its own devices for a while. Show G that there is activity going on (i.e. they index the new content) and slowly begin to build some good quality links over the next couple of weeks. Then it is time to turn up the power (improving your link graph - upwards) whilst at the same time adding regular content (content graph also trending upwards).
Following this ensures that your new found popularity is natural in appearance and you will find that rankings will begin to improve.
One final thing - remember to link to your new content (inner pages) as well as the home page. Make use of the great advice here around GWT and keywords as anchor text and before long G will accept the tsunami of links incoming to your ever so popular website!
If all this was true, it would be a hell of an easy job to punish your competitor websites.
I do agree with linking to the inner pages though and have been doing that for a few weeks now. Each new page will rank better for different keywords, so it makes sense to promote them all individually.