Does a South African refugee travel document holder need a transit visa for Germany or the Netherlands?

Given that you hold a refugee travel document, the following are the rules, as stated in Timatic, the database used by airlines:

For Germany:

Visa required, except for Nationals of Afghanistan, Bangladesh, Congo (Dem. Rep.), Eritrea, Ethiopia, Ghana, India, Iran, Iraq, Lebanon, Mali, Nigeria, Pakistan, Somalia, South Sudan, Sri Lanka, Sudan, Syria or Turkey holding onward tickets in transit AND:

holding a valid visa issued by Bulgaria, Canada, Croatia, Cyprus, Ireland (Rep.), Japan, Romania, USA or United Kingdom traveling to any non-Schengen Member State;

A max. transit time of 24 hours through Frankfurt (FRA) or Munich (MUC).

On the same day between 04:30 and 23:30 through Hamburg (HAM).

On the same day between 04:30 and 23:00 through Cologne/Bonn (CGN).

On the same day between 06:00 and 21:00 through Dusseldorf (DUS). Inbound carrier must provide prior notice to authorities in Dusseldorf (DUS) by fax: +49 211 421 20521; tel: +49 211 421 63695 or SITA Telex DUSOVXH.

On the same day between 06:00 and 23:00 through Berlin Tegel (TXL), provided connection time is at least 75 minutes. Inbound carrier must provide prior notice to the handling agent at Berlin Tegel (TXL) by fax or SITA Telex and the airport authorities by SITA Telex (TXLVZXH). This must include the passenger's name, itinerary, date, nationality and seat number. The passenger is not permitted to travel with animals carried in the cabin or in the cargo hold (AVIH).

So, because you have a Canadian visa, you do not need an airside transit visa for Germany

For the Netherlands:

Transit without a visa is not allowed for holders of Refugee Travel Documents not issued by an EEA Member State, Switzerland or USA

Except for holders of a Refugee Travel Document and a permanent residence permit issued by Canada and holding onward tickets transiting by the same or first connecting aircraft.

So, if you are a permanent resident of Canada, you do not need an airside transit visa for the Netherlands. Otherwise, you do need it.

Nationals of DR Congo ordinarily need an airport transit visa to transit through the international transit area in any Schengen airport. It appears to be immaterial for this requirement that your travel document is issued by South Africa (whose own citizens do not require airport transit visas).

However, there's an exemption for holders of valid visas for Canada, Japan, USA or a non-Schengen EU country, when they are on their way to or from that country. So you should be fine IF you're actually transiting to or from Canada.