If you're interested in increasing the maximum number of windows, there are four lines in two files within Browser.apk that need to be modified.
I made these changes to the HTC Browser.apk from VaelPak 3.2 RC 1, but it should work on any HTC Browser. 0x10 is 16 in hex, so you can make this value whatever you want. If you get above 25 or so open windows, the browser tends to crash.
Line 52: Change "const/4 v2, 0x4" to "const v2, 0x10"
Line 565: Change "const/4 v0, 0x4" to "const v0, 0x10"
Line 618: Change "const/4 v1, 0x4" to "const v1, 0x10"
Line 658: Change "const/4 v3, 0x4" to "const v3, 0x10"
Once you know where to look, the changes are pretty easy with APKTool (just use version 1.3.1, since 1.3.2 has a bug and doesn't seem to work correctly).
Here is an HTC Browser.apk with these changes, along with some LowRider menu icons thrown in.
EDIT: This is not an installable apk, because the certificates won't match. You need to have a rooted phone and use ADB to overwrite /system/app/Browser.apk (Make a backup first, of course.)