I'd say, it depends on:
1) where you want to connect: MUC (fast), FRA (can be hectic) or IST (no comment);
2) when you want to arrive;
3) whether you are willing to fly purely on LH/ TK or on mix of LH/TG;
4) if you are OK with a sudden chance of an aircraft (with TK);
5) food: tastes differ;
6) seats: --> see point 4 plus do some basic search on Turkish forum; they have at least 4 threads dedicated to IST-BKK; and on setguru there are several posts about C seats of LH and TK. It's easy to make a comparative overview of them.
7) on airliners.net there are two very recent reports of AMS-IST-BKK with TK in C and several reports of FRA-BKK on LH in C, too.
8) there is a thread here dedicated to what you can expect on intercontinental flights in C.