The CD contains a DDR2 example in the DE3_demonstrations folder. Here are the connections to/from the NIOS given in verilog:
.clk(OSC1_50),
.reset_n(system_reset_n),
.in_port_to_the_pio_button(Button),
.out_port_from_the_pio_led({LEDR, LEDG, LEDB}),
.global_reset_n_to_the_altmemddr(system_reset_n),
.local_init_done_from_the_altmemddr(),
.local_refresh_ack_from_the_altmemddr(),
.local_wdata_req_from_the_altmemddr(),
.mem_addr_from_the_altmemddr(mem_addr[12:0]),
.mem_ba_from_the_altmemddr(mem_ba[1:0]),
.mem_cas_n_from_the_altmemddr(mem_cas_n),
.mem_cke_from_the_altmemddr(mem_cke[0]),
.mem_clk_n_to_and_from_the_altmemddr(mem_clk_n),
.mem_clk_to_and_from_the_altmemddr(mem_clk),
.mem_cs_n_from_the_altmemddr(mem_cs_n[0]),
.mem_dm_from_the_altmemddr(mem_dm),
.mem_dq_to_and_from_the_altmemddr(mem_dq),
.mem_dqs_to_and_from_the_altmemddr(mem_dqs),
.mem_dqsn_to_and_from_the_altmemddr(mem_dqsn),
.mem_odt_from_the_altmemddr(mem_odt[0]),
.mem_ras_n_from_the_altmemddr(mem_ras_n),
.mem_we_n_from_the_altmemddr(mem_we_n),
.oct_ctl_rs_value_to_the_altmemddr(),
.oct_ctl_rt_value_to_the_altmemddr(),
.reset_phy_clk_n_from_the_altmemddr(),
.out_port_from_the_ddr2_i2c_scl(mem_SCL),
.bidir_port_to_and_from_the_ddr2_i2c_sda(mem_SDA)