Good question. The answer is whatever works best. Here are a few criteria that you should look at when choosing a template.
Front page
Add placement
Commenters section
Good Navigation
Is easily customizeable.
Is it SEO friendly
Pleasing colors
Front Page
Many new themes are being built with what they call a magazine layout. The actuall blog is placed at /blog and the main page at / is a landing page in a sense to show as many posts as possible and maximize the ad space. Because after all if you are tryingto get new users, it is better to give them a wider selection of posts to choose from. This may actually help you gather more readers. The front page isn’t neccessary, but a lot of the big bloggers have them. I may go that route eventually, but not yet. It’s still something to consider though.
Add placement
Add placement is always important. You want to be able to have a place that you can display your 125×125 ads and Google Adsense or YPN. You will also want a place to store any text link ads, such as “featured sites” and perhaps a banner at the top. You can even place ads in your RSS feed.
There are many areas in a theme that you can place ads, some themes have these already built in, which is nice. It is nice to have to figure out how to add ads to different areas of your site. Now at some level you will have to do this yourself. It’s very difficult almost impossible to find a theme that has multiple ad positions built into it.
Commenters section
A top commenters section is a good thing to have. I haveseen a Wordpress plugin for recent comments, but not top comments. I’m sure there is one out there. If not you may have to have it built for you. But the top commenters section is a place where you can let your commenters share some of your popularity. This allows them to gain some off-site clicks to their own sites. For beginner blogs its not neccessary until you get some people commenting on your blog. There is no need to advertise that your blog is a ghost town.
Good Navigation
One of the reasons I choose the superAdsense theme is because of the built in Adsense and Clickbank capabilities. I also chose it because it had a good navigation bar at the top that easily showed any pages that I added through Wordpress. I can also go directly to the theme and add a non-Wordpress link into the navigation area where the other pages have been added. It’s easy and simple. One less thing I have to concern myself with.
Easily Customizable
If you need to look at the code for more than 10 to 20 minutes to figure out what is going on, its too complicated. Now this could be because you are a novice when it comes to programming or it could really be that difficult. Choosing a theme that you can easily customize will make it a lot easier to expand your blog or site as yoursite grows.
Pleasing Colors
If you have a garden theme you probably don’t want to use purple. That’s basic stuff, but you should grab something that is somewhat neutral but also asthetically pleasing. Look online to find some netural color palettes.