Special note about Pooler’s cpuminer for Litecoins (https://bitcointalk.org/index.php?topic=55038.0) – Bitcoin Miners in Tray can run and control it, but due to two quirks, no output from cpuminer is displayed until it is stopped. Cpuminer directs all of its output to stderr, which BMT handles well. However, it does not finish output of a line when a line is written to stderr, thus all lines are dumped on the pipe at the same time when cpuminer stops and closes its streams. There is nothing I can do about it, as this needs to be fixed by Pooler.

CGMiner (https://bitcointalk.org/index.php?topic=28402.0) must be started with --text-only or -T parameter to disable ncurses and with --log 1 or -l 1 to log output every second. CGMiner suffers from the same problem as pooler’s cpuminer, which is not strange as it was forked from it. The problem is however only with the redirected stdout stream, while stderr works fine, outputting the lines as they are pushed into the pipe. Once CGMiner is stopped, all text on stdout will be dumped in one go. -l 1 seems to fix this.

@CapnGimp: Experiment with the command line settings in a cmd.exe window. Once you are satisfied with the settings, copy them to the config file. You can also play with the settings in directly in the config file and hit reload config, which will reinitialise both the program and restart all the enabled miners.
Yes, keep-alive will auto-restart the miner, if the miners terminates by itself or if there is no output coming from the miner on stdout and/or stderr. I haven't had any issues with poclbm dying either, but I implemented keep-alive as a safety net, because I want a 100% unattended system.
I am still not on Stratum, so cannot advise on -a parameter.