Here are some ideas if you don't know what to write your thesis or similar work about or just want to perform some interesting research. I wish I had time to work on them; unfortunately, I have time only for a small fraction.

• An audio+video conferencing multiplatform application providing end-to-end encryption
• Code injector (proxy that injects your code to executable files transferred over insecure link)
• How to make basic chemicals like nitrates or antibiotics in amateur conditions when an apocalypse (e.g. nuclear war) occurs; can contain own experiments
• Cheap extraction of important ensymes and chemicals for genetic engineering (thermostable DNA-Polymerase, EcoRI, dNTPs) at home without buying them online
• Exporting steganographic bits (least significant bits or noise) from WAVs and RAW photos as a block device. Linux nbd seems pretty simple.
• Finish dm-steg.
• Open-source ocl-hashcat. Their license policy and DRM are simply unacceptable.
• OsmocomBB "mobile" application sucks. Go fix it.
• Silicon engineering: An Open Source Trusted Platform Module
• Portable multiplatform encryption of a flash drive. Current solutions (TrueCrypt) require admin/root access to install and setup. However, for example an encrypted WebDAV service can be run from unprivileged userspace.
• Build a HFCC vest. Commercial implementation cost $10k. Could it be build for one tenth of that price?
• rtl-sdr showed us that crappy SDR can cost $10. However, much better A/D converters are sold for similar price in China. Can a better SDR be build for an affordable price?
• Write decoder and cracker for MOTOTRBO (it's 40-bit ARCFOUR), build open-source sdr-based client for GSM and Tetra.
• Investigate possibilities of radio transmitting using graphic card. Create a gnuradio sink for transmitting arbitrary signals.
• Create an implementation of GNSS satellites (NAVSTAR, GALILEO, GLONASS) that runs on customer-grade FPGA and SDR.
• Implement some nice app-level isolation framework into Linux (like Qubes OS)
• Fork Firefox. Fix all that NSA "features" and nasty bugs.
• Create sdr-based implementation of TAMARA or VERA passive sensor. Is it possible to fingerprint individual transmitters like rumors about ASMKS say?
• Implement some nice GUI for Bitcoin Contracts
• BadBIOS is a hoax. Can be a similar malware really build?
• Implement cryptoanarchy procedures described here (Czech only, sorry)
• Build a decentralized, censorship-resistant and surveillance-free distributed web search engine. YaCy could be a good starting point
• A decent MITM suite for SSHv2 would be cool. Exploiting SSH agent would be even cooler.
• Implement checksums and error correction to Linux md-raid.
• navigation software that recommends you speed such that you don't have to wait on traffic lights
• or just pick one here ;)