1) I have added a directory on one of my sites, this is supposed to be a useful resource, i want the companies i linked to to link back. I will see a sudden surge in links due to this but the site is better as a result of my directory, why should that be punished.
Those things are typically more of an "anchor" in the true sense of the word. Get rid of it if you can.
2) New sites that are of interest to people may see sudden surges in links as the buzz about them takes off, would such sites be punished? i think not.
There are Google Patents that discuss this in great detail. All sites have a profile. Here is one excerpt from one of those patents...
59. The method of claim 58, wherein the adjusting the ranking includes penalizing the ranking if the longevity indicates a short life for the linkage data and boosting the ranking if the longevity indicates a long life for the linkage data.
3) i have old sites which dont have many links, i suddenly am putting hours of work into them and i expect links to take off for them, will this sudden surge harm me?
It may or may not. If the type of surge is related to the type of activity you describe above, I don't think there will be much credit given. And, since you have that "anchor" attached to your site, your going to provide the final piece of closing the loop, a link back. That should cause some issues. ;)
4) I used to be prominent in seo 4 years ago, i sold up and had a break. Now im back the question arises of how is a webmaster supposed to make any serious money out of a site within a year assuming that youre not allowed to prosper with incoming links too fast?
Do something better than everyone else. If you don't do it better, you're going to end up like "most" everyone else, struggling for bits and pieces of the bone.