I generally associate negative connotations with so-called, as in the "so-called free world". I wouldn't use it just to name something, as in "the kernel is written in the so-called C language". so-called implies "it's called this, but it's not".
Two imo dubious occurrences in the install notes. It's not a so-called MBR partition; it is an MBR partition. Similarly with hppa LIF. There's one other use in loongson about initrd which seems ok. (There is another definition of so-called which isn't negative, as in "if you want a great OS check out OpenBSD, so-called because the source is all open". But that's not how so-called is used below.) Index: m4.common =================================================================== RCS file: /cvs/src/distrib/notes/m4.common,v retrieving revision 1.99 diff -u -p -r1.99 m4.common --- m4.common 4 Dec 2013 23:20:19 -0000 1.99 +++ m4.common 25 Jan 2014 00:54:18 -0000 @@ -477,8 +477,8 @@ dnl Describes MBR partitioning. So much dnl duplicated 5 times. dnl define({:-OpenBSDInstallMBRPart1-:}, -{:- Disks on OpenBSD/MACHINE are partitioned using the so-called - ``MBR'' partitioning scheme. You will need to create one +{:- Disks on OpenBSD/MACHINE are partitioned using the ``MBR'' + partitioning scheme. You will need to create one MBR partition, in which all the real OpenBSD partitions will be created.-:})dnl dnl Index: hppa/install =================================================================== RCS file: /cvs/src/distrib/notes/hppa/install,v retrieving revision 1.24 diff -u -p -r1.24 install --- hppa/install 4 Dec 2013 23:20:19 -0000 1.24 +++ hppa/install 25 Jan 2014 00:54:33 -0000 @@ -47,7 +47,7 @@ Booting from Network: reasonably portable to other UN*X-like operating systems. More information on diskless booting can be found in the OpenBSD diskless(8) manual page. - Your MACHINE expects to be able to download a so-called LIF (``Logical + Your MACHINE expects to be able to download a LIF (``Logical Interchange Format'') image, containing both the boot code and the kernel, via the HP rboot protocol, for older firmware, or via the bootp protocol, for more recent firmware.