While I haven't yet picked out an app to use for full-time eBook reading, being a 3G user running 3.1.3 I've been using the //nav/transfer method to upload my books to Bluefire, and I found the whole process so enjoyable I had to set myself up a home screen shortcut which would directly boot the server tool.
The process is mildly complicated and, as far as I could tell, impossible to do without a jailbreak--I really tried, too--but it results in a clean looking "app" style button appearing on my home screen and happily sitting beside the Bluefire app. As you can see, I called the shortcut "Redserver", largely in deference to the icon, which itself is only red because I lack the artistic ability to do any better than a recolor. I toyed with calling it Redice but preferred to use something meaningful.
As for the particulars: it's simply a Safari home screen bookmark. These are typically done by visiting a page, hitting the + button, and selecting "Add to Home Screen". Unfortunately, visiting any bluefirereader:// "protocol" links takes you to BR immediately, so you don't get an opportunity to add it as either a bookmark or home screen shortcut. While you can enter a bookmark for it manually, you can't add a bookmark to the home screen, so that's not the path I took.
Instead, I added a home-screen link to Google just to see if the results would be easily manipulated. Navigating the (jailbroken) iPhone's filesystem, I found the Google shortcut had written itself to /private/var/mobile/Library/WebClips/{LONG HEX SEQUENCE}, as a PNG icon and XML (and ASCII, thankfully) plist. I did a quick edit of the Bluefire icon to turn it red and add the standard gloss finish and rounded edges, and edited the plist to point to "bluefirereader://nav/transfer" with the name "Redserver". I edited the IconURL too, to point to a non-existent icon on the Bluefire Reader web page, but only because it's what Apple would have done; it has no actual impact.
If anyone else wants to try this (and of course, any negative results incurred as a result of blah blah blah not my fault), here's my icon and plist. I recommend creating a home screen shortcut using Safari first and replacing its contents with these rather than trying to add it from scratch, mainly because of the {LONG HEX SEQUENCE} part of the file structure, the importance of which I am unsure of but which is probably best handled by iPhone rather than human.