I used to be afraid of check-raising the flop in a spot like this.
It felt like I was turning my hand into a bluff, because if he called,
I wouldn't know if it was with a Q or a draw or a worse pair or a total
float. Then I'd check the turn, and he'd bet, and I wouldn't know what
to do, then I'd call if it wasn't a spade (nevermind that I'm rarely
checking a flush myself on the turn), then the river would be like a
spade or an Ace or a King and I'd check and he'd bet and I'd fold and
feel stupid, like I should have just check-called the flop.

Increasingly, though, I've come to realize that your opponents only
get dealt so many hands and only have so many options with them. If he
really is calling the flop with all that stuff, then you're way ahead
of his range. Plus, you have at least some idea of which turn cards
will improve, not his specific hand, but the equity that his full range
against you. And when you get a relatively safe turn, you usually know
it, and you can even raise again:

No-Limit Hold'em, $10.00 BB (6 handed) - Hold'em Manager Converter Tool from FlopTurnRiver.com

UTG ($1052)
MP ($1076)
CO ($1042)
Button ($761.60)
Hero (SB) ($1005)
BB ($1639.55)

Preflop: Hero is SB with 9, 9
2 folds, CO bets $30, 1 fold, Hero calls $25, 1 fold

Flop: ($70) Q, 3, 6 (2 players)
Hero checks, CO bets $50, Hero raises $123, CO calls $73

Turn: ($316) 5 (2 players)
Hero checks, CO bets $200, Hero raises $852 (All-In), CO calls $652

River: ($2020) 4 (2 players, 1 all-in)

Total pot: $2020

Results:
Hero had 9, 9 (one pair, nines).
CO had 6, A (one pair, sixes).
Outcome: Hero won $2017

Granted this second raise is a lot thinner, but in my opinion it's
better than check-calling. I at least haven't yet figured out how to
turn a profit on the river if I just check-call the turn here, which
means it's to my advantage to end the hand now. I doubt I'm ahead of
Villain's calling range, but as you see, he can call worse. Not to
mention that since most people don't expect the double check-raise,
they'll open themselves up to getting blown off of a draw by betting it
when you check. That means there's a lot of value in picking up the pot
on the turn rather than giving Villain the opportunity to realize what
is often substantial equity on the river.

Oh, and this has the added value of strengthening your generally very weak check-raise-check range.