Flips

Creates the smallest BPS patches of any known tool in existence, and is faster than any other comparable creator
Creates the smallest IPS patches of any known tool in existence, too (but only a little smaller, Lunar IPS is quite good)
Fully-featured GUIs under Windows and GTK+, including command line support; can also be a pure command line program
Can apply multiple patches to the same ROM, creating a huge pile of ROMs (GUI only)
Can remembers which ROMs you've used, and use them again if it thinks it's correct (BPS only, GUI only)
Can launch other programs after patching the ROMs; together with the above, this allows you to double click a BPS to launch an emulator (GUI only)

Planned features:

Better autodetection for CLI apply/create; if the first one is a patch, apply, else create
Better support for ROM database in CLI; the -d flag, or DB enabling from the GUI (for pure-CLI, existence of flipsdb.bin file beside Flips), will store ROMs in the database; the filename "." will read from it, and "wrong ROM" will look for the right one (but not automatically use it)
Use path of patch as output filename, not the ROM path
Replace Settings button with Advanced, which switches to a different UI
Remove emulator chooser, use OS file associations instead
Automatic source ROM chooser for creation

Not planned (if your plans are different, send a PR):

OSX GUI support; there's a third-party fork here, and MultiPatch exists and the Windows version works in Wine. I can't test OSX stuff well enough to merge that fork, so pick your favorite.
Qt GUI support; my distro prefers GTK+, and all distros I've seen can run both GTK+ and Qt, not worth the effort (and QString's UTF-16 irritates me)

Compilation - Linux (Debian/Ubuntu):

sudo apt-get install g++ build-essential; for GUI support, also sudo apt-get install libgtk-3-dev pkg-config
./make.sh to build an optimized binary; for development, use make CFLAGS=-g

Compilation - other Linux:

Install make and g++; for GUI support, also install pkg-config and GTK+ 3 headers; for profiling support, also install curl or wget
./make.sh to build an optimized binary; for development, use make CFLAGS=-g

Compilation - OSX and other Unix:

Install a C++ compiler
clang++ *.c *.cpp -O3 -o flips (with changes as appropriate)
For GTK GUI support, use some suitable variant of clang++ *.c *.cpp -O3 -o flips -DFLIPS_GTK -lgtk3
For better optimizations (profiling/etc), extract the appropriate commands from Makefile and make.sh

Compilation - Windows:

Install mingw-w64
mingw32-make CFLAGS=-O3 (GUI is automatically enabled), or extract the appropriate optimization commands from make.sh
Alternatively, here's a binary.

Usage:

If GUI is enabled, just run the program. File pickers' window titles tell what they want; Enable automatic ROM picker and Run in Emulator can cause file pickers to appear and disappear depending on the chosen patch, making usage less predictable, so it's disabled by default.
For CLI use, see ./flips --help. Available both with or without GUI support (though Windows CLI use from interactive prompts is slightly screwy, due to OS limitations).