I use a variant of the Motorola freeware assembler which I modified a bit for my purposes (e.g. it understands include files now).
The Special-Bootstrap mode is a very handy feature of the 68HC11 - I just
could not find any loader programs for Linux and therefore wrote my own (that
was about in 1994 when Linux was not as popular as it is today).
It's a console application that takes just the S19 file as argument.
It then asks you to press reset on your 68HC11 board.
As soon as it detects the reset (by receiving the break code the 68HC11 sends
when the bootloader in the ROM is ready), it sends the upload code and
then starts the upload.
Recently, I updated my hc11loader to work also with USB to RS-232 converters.
The problem with those is the timing when sending the firmware byte by byte.
The occurring delays when doing so causes the bootloader in the 68HC11 ROM
to assume the upload being complete, therefore aborting the upload and
starting a incomplete program.
I avoid such pauses by sending the data block wise, thus making sure the buffer
of the USB to RS-232 converter never goes empty unless the are no more data
to send.
Unless you have very old hardware (8250), this should also work with
"normal" RS-232 ports (16550A).
I might add an option to disable the buffering, tough.
You find my hc11loader as part of my devtools (see downloads below)
In 1990, I used to work with pcbug11, but this DOS program does not work on
newer PC hardware.
Since I again could not find any alternatives, I again started
to write my own program as replacement for pcbug11.
But I have to disappoint you, it never got finished.
It's included in my devtools package, so you can play around with it
(it basically works: It supports reading and writing of the 68HC11 memory and
registers - most important, the user interface is missing).