Developer not Marketer, and I could use your help.

I am a developer for a small company. I am very familiar with On-Site SEO because I am the one coding the sites most of the time. But my company is trying to hire someone to handle internet marketing when if I could come up with a link strategy I could get a significant raise.

I want to build a link structure to pass on the link juicage, im sure a lot of you have services to recommend to do this, but I'd (and my company) rather do it on my own, do you have any advice for this newb?

Do you have a budget for software?
Or does it have to be completely free?

I could get the funds if they were well spent, but with my knowledge of Ruby on Rails i'm sure I could program most easy tasks if it was just automating something. Hope this helps.

The easiest boost you can get is social bookmarking. With social bookmarking you will see an instant rise in your ranking (24-48h if you site is indexed). Onlywire is a good free tool but you will need to do all the account registration manually.
In terms of tools you can use SEnuke and XGen SEO to get good backlinks. Scrapebox is very good but with your knowledge I would be a bit cautious before using it.
SEnuke and XGen SEO have free trials you could try and there is a cracked version of XGen SEO in the downloads section if you don't mind using pirated software.

My advice:

Assuming you have the skills to develop nearly anything, seek out a proven SEO. I am sure you could have him map out his "dream" seo system if you offered him a copy of it.

Try posting in the JV section on this forum to see if anyone would be interested.

If this doesn't appeal to you, or if you are unable to give away a copy of something you developed under your companies time. Perhaps even pay a consultant to map out and design its operations.

You also may find this to be an interesting read: http://www.bluehatseo.com/seo-empire-part-1/

you fried my brain with all of this, kudos rare feat.