Analyze, Browse, Command, Edit, Encrypt and Scan for the common use. If you take 6 in all, it'll cost 3,600¥.
For hacking, I'd go with Armor, Attack, Blackout, Corrupt, Decrypt, Defuse, ECCM, Exploit, Medic, Nuke, Sniffer, Spoof, and Stealth. At rating 6, they'd be 78,000¥ total.
That leaves 38,400¥. Two Agents (R6) is 30,000¥, leaving 8,400¥.
Are you sure you have 120,000¥ for programs, or is it for resources? It seems like an awful lot.