Heat maps are definately relevant no matter what the size of your user base. Even with single user applications by understanding they way they use the software you can optimise it for them. As you say however you have to take different approaches. For larger user bases you need to make it highly analytical, you can not allow for and subjectivity. Focusing on your userbase however there are several tools you could use
Google Analytics (I use this lots)
Built in to Analytics you have "In Page" options, this allows you to understand where users are clicking through your website.
CrazzyEgg (Never used but heard good things)
CrazzyEgg claims to go beyond what Google Analytics offers by showing you data such as where users stop scrolling.
Click Tail (Used a while ago)
If you are able to use methods such as Hallway Testing then this software will give you very detailed information about how users position their mouse, which is often a indication of where they are looking. This is especially effective for small user basis.
When using heat maps remember:
No matter your user size, you need a large amount of data to make it reliable
If possible use a control, such as a competing website. If I were to make a forum I would try to look at how good examples such as UX produce high conversions.
A/B Test. This isn't about your improvements you make. Test between different software packages, for example if X loads really slowly it could slow your whole site, thus making users change the way they use the site.
This article on CGMA has helpful information about more Dos and Don'ts. Not software related but still relevant
Don't make them over complicated. Keep the heat ranges simple, you want to see where people look and where they don't, it is much easier to work on this unless you have huge amounts of time to analyse it. Look at the examples below, simpler means much easier to understand.