I am looking for a sefer that offers an in depth explanation of tosafos (and preferably rashi) to aid me in studying in depth on my own. The ideal would be to have it in english, but a hebrew explanation would suffice as well. My question is what are my options for such a sefer, and which option is the most comprehensive and clear.
Mesivta is a running Hebrew commentary with footnotes which includes a full explanation of Rashi Tosfos and the major issues and how the Rishonim and Achronim deal with it
It has about 120 volumes covering all of Shas.
You can view some of its features here http://www.oz-vehadar.com/en/department/16/editions-of-the-metivta
The Daf Yomi Advancement Forum - dafyomi.co.il - has an English point-by-point translation of every Tosfos in the Maseches, in its entirety.
They cover the entire Shas until the end of Avoda Zara - and I'm sure they are working on the last few Mesachtot.
Each Tosfos starts with a summary, and then each phrase is brought in the original and then explained in English.
There is a set of Shaarei Tosafos which explains each Tosafos, in Hebrew, really well.
Mei Menuchos, by Rabbi Nachman Kahana, is a clear and systematic explanation of Tosfos (in Hebrew), and is available free online for several mesechtos:
Artscroll has many but not all tosfos explained in footnotes.